PDB entry 3cma

View 3cma on RCSB PDB site
Description: The structure of CCA and CCA-Phe-Cap-Bio bound to the large ribosomal subunit of Haloarcula marismortui
Class: ribosome
Keywords: RIBOSOME 50S, PROTEIN-PROTEIN COMPLEX, RNA-RNA COMPLEX, PROTEIN-RNA COMPLEX, PEPTIDYL-tRNA HYDROLYSIS, RIBOSOME
Deposited on 2008-03-21, released 2008-09-23
The last revision prior to the SCOPe 2.01 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-25.
Experiment type: XRAY
Resolution: 2.8 Å
R-factor: 0.194
AEROSPACI score: 0.28 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '0':
    Compound: 23S ribosomal RNA
    Species: Haloarcula marismortui [TaxId:2238]
  • Chain '1':
    Compound: 50S ribosomal protein L37e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cma11
  • Chain '2':
    Compound: 50S ribosomal protein L39e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cma21
  • Chain '3':
    Compound: 50S ribosomal protein L44E
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cma31
  • Chain '5':
    Compound: RNA (5'-r(*cp*cp*a)-3')
  • Chain '6':
    Compound: RNA (5'-r(*cp*cp*(8an))-3')
  • Chain '9':
    Compound: 5S ribosomal RNA
    Species: Haloarcula marismortui [TaxId:2238]
  • Chain 'A':
    Compound: 50S ribosomal protein L2P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: 50S ribosomal protein L3P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cmab1
  • Chain 'C':
    Compound: 50S ribosomal protein L4P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed):
  • Chain 'D':
    Compound: 50S ribosomal protein L5P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cmad1
  • Chain 'E':
    Compound: 50S ribosomal protein L6P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: 50S ribosomal protein L7Ae
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cmaf1
  • Chain 'G':
    Compound: 50S ribosomal protein L10e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed):
  • Chain 'H':
    Compound: 50S ribosomal protein L10e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cmah1
  • Chain 'I':
    Compound: 50S ribosomal protein L11P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cmai1
  • Chain 'J':
    Compound: 50S ribosomal protein L13P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cmaj1
  • Chain 'K':
    Compound: 50S ribosomal protein L14P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cmak1
  • Chain 'L':
    Compound: 50S ribosomal protein L15P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cmal1
  • Chain 'M':
    Compound: 50S ribosomal protein L15e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed):
  • Chain 'N':
    Compound: 50S ribosomal protein L18P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cman1
  • Chain 'O':
    Compound: 50S ribosomal protein L18e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cmao1
  • Chain 'P':
    Compound: 50S ribosomal protein L19e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cmap1
  • Chain 'Q':
    Compound: 50S ribosomal protein L21e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cmaq1
  • Chain 'R':
    Compound: 50S ribosomal protein L22P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cmar1
  • Chain 'S':
    Compound: 50S ribosomal protein L23P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cmas1
  • Chain 'T':
    Compound: 50S ribosomal protein L24P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cmat1
  • Chain 'U':
    Compound: 50S ribosomal protein L24e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cmau1
  • Chain 'V':
    Compound: 50S ribosomal protein L29P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cmav1
  • Chain 'W':
    Compound: 50S ribosomal protein L30P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cmaw1
  • Chain 'X':
    Compound: 50S ribosomal protein L31e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cmax1
  • Chain 'Y':
    Compound: 50S ribosomal protein L32e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3cmay1
  • Chain 'Z':
    Compound: 50S ribosomal protein L37Ae
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed):
    • PDB 3CMA
    Domains in SCOPe 2.01: d3cmaz1
  • Heterogens: PHE, MG, NA, SR, CL, K, CD, HOH

PDB Chain Sequences:

  • Chain '0':
    No sequence available.

  • Chain '1':
    Sequence, based on SEQRES records: (download) 
    >3cma1 (1:)
mtgagtpsqgkknttthtkcrrcgeksyhtkkkvcsscgfgksakrrdyewqskage

    Sequence, based on observed residues (ATOM records): (download) 
    >3cma1 (1:)
tgagtpsqgkknttthtkcrrcgeksyhtkkkvcsscgfgksakrrdyewqskage

  • Chain '2':
    Sequence, based on SEQRES records: (download) 
    >3cma2 (2:)
mgkkskatkkrlakldnqnsrvpawvmlktdrevqrnhkrrhwrrndtde

    Sequence, based on observed residues (ATOM records): (download) 
    >3cma2 (2:)
gkkskatkkrlakldnqnsrvpawvmlktdrrnhkrrhwrrndtde

  • Chain '3':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3cma3 (3:)
mqmprrfntycphcnehqehevekvrsgrqtgmkwidrqrernsgigndgkfskvpggdk
ptkktdlkyrcgecgkahlregwragrlefqe

  • Chain '5':
    No sequence available.

  • Chain '6':
    No sequence available.

  • Chain '9':
    No sequence available.

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >3cmaB (B:)
mpqpsrprkgslgfgprkrstsetprfnswpsddgqpgvqgfagykagmthvvlvndepn
spregmeetvpvtvietppmravalrayedtpygqrpltevwtdefhseldrtldvpedh
dpdaaeeqirdaheagdlgdlrlithtvpdavpsvpkkkpdvmetrvgggsvsdrldhal
divedggehamndifrageyadvagvtkgkgtqgpvkrwgvqkrkgkharqgwrrrignl
gpwnpsrvrstvpqqgqtgyhqrtelnkrlidigegdeptvdggfvnygevdgpytlvkg
svpgpdkrlvrfrpavrpndqprldpevryvsnesnqg

    Sequence, based on observed residues (ATOM records): (download) 
    >3cmaB (B:)
pqpsrprkgslgfgprkrstsetprfnswpsddgqpgvqgfagykagmthvvlvndepns
pregmeetvpvtvietppmravalrayedtpygqrpltevwtdefhseldrtldvpedhd
pdaaeeqirdaheagdlgdlrlithtvpdavpsvpkkkpdvmetrvgggsvsdrldhald
ivedggehamndifrageyadvagvtkgkgtqgpvkrwgvqkrkgkharqgwrrrignlg
pwnpsrvrstvpqqgqtgyhqrtelnkrlidigegdeptvdggfvnygevdgpytlvkgs
vpgpdkrlvrfrpavrpndqprldpevryvsnesnqg

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >3cmaD (D:)
mssesesggdfhemrepriekvvvhmgighggrdlanaedilgeitgqmpvrtkakrtvg
efdiregdpigakvtlrdemaeeflqtalplaelatsqfddtgnfsfgveehtefpsqey
dpsigiygldvtvnlvrpgyrvakrdkasrsiptkhrlnpadavafiestydvevse

    Sequence, based on observed residues (ATOM records): (download) 
    >3cmaD (D:)
fhemrepriekvvvhmgighanaedilgeitgqmpvrtkakrtvgefdiregdpigakvt
lrdemaeeflqtalplaelatsqfddtgnfsfgldvtvnlvrpgyrvakrdkasrsiptk
hrlnpadavafiestydvev

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >3cmaF (F:)
mpvyvdfdvpadleddalealevardtgavkkgtnettksiergsaelvfvaedvqpeei
vmhipeladekgvpfifveqqddlghaaglevgsaaaavtdageadadvediadkveelr

    Sequence, based on observed residues (ATOM records): (download) 
    >3cmaF (F:)
pvyvdfdvpadleddalealevardtgavkkgtnettksiergsaelvfvaedvqpeeiv
mhipeladekgvpfifveqqddlghaaglevgsaaaavtdageadadvediadkveelr

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >3cmaH (H:)
msdkpasmyrdidkpaytrreyitgipgskiaqhkmgrkqkdaddypvqisliveetvql
rhgsleasrlsanrhlikelgeegdykmtlrkfphqvlrenkqatgagadrvsdgmraaf
gkivgtaarvqageqlftaycnvedaehvkeafrraynkitpscrikvergeellia

    Sequence, based on observed residues (ATOM records): (download) 
    >3cmaH (H:)
kpasmyrdidkpaytrreyitgipgskiaqhkmgrkqkdaddypvqisliveetvqlrhg
sleasrlsanrhlikelgeegdykmtlrkfphqvlrenkdgmraafgkivgtaarvqage
qlftaycnvedaehvkeafrraynkitpscrikvergeel

  • Chain 'I':
    Sequence, based on SEQRES records: (download) 
    >3cmaI (I:)
magtievlvpggeanpgpplgpelgptpvdvqavvqeindqtaafdgtevpvtvkydddg
sfeievgvpptaelikdeagfetgsgepqedfvadlsvdqvkqiaeqkhpdllsydltna
akevvgtctslgvtiegenprefkeridageyddvfaaeaqa

    Sequence, based on observed residues (ATOM records): (download) 
    >3cmaI (I:)
gvpptaelikdeagfetgsgepqedfvadlsvdqvkqiaeqkhpdllsydltnaakevvg
tctslgvtie

  • Chain 'J':
    Sequence, based on SEQRES records: (download) 
    >3cmaJ (J:)
msvaefdadvivdardcimgrvasqvaeqaldgetvavvnaeravitgreeqivekyekr
vdigndngyfypkrpdgifkrtirgmlphkkqrgreafesvrvylgnpydedgevldgts
ldrlsnikfvtlgeisetlganktw

    Sequence, based on observed residues (ATOM records): (download) 
    >3cmaJ (J:)
aefdadvivdardcimgrvasqvaeqaldgetvavvnaeravitgreeqivekyekrvdi
gndngyfypkrpdgifkrtirgmlphkkqrgreafesvrvylgnpydedgevldgtsldr
lsnikfvtlgeisetlganktw

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3cmaK (K:)
mealgadvtqglekgslitcadntgarelkvisvhgysgtknrhpkaglgdkitvsvtkg
tpemrrqvleavvvrqrkpirrpdgtrvkfednaavivdenedprgtelkgpiarevaqr
fgsvasaatmiv

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >3cmaL (L:)
mtskkkrqrgsrthgggshknrrgaghrggrgdagrdkhefhnheplgksgfkrpqkvqe
eaatidvreidenvtllaaddvaevedggfrvdvrdvveeaddadyvkvlgagqvrhelt
liaddfsegarekvegaggsveltdlgeerqaeaeetedadadee

    Sequence, based on observed residues (ATOM records): (download) 
    >3cmaL (L:)
tskkkrqrgsrthgggshknrrgaghrggrgdagrdkhefhnheplgksgfkrpqkvqee
aatidvreidenvtllaaddvaefrvdvrdvveeaddadyvkvlgagqvrheltliaddf
segarekvegaggsveltdlgeerq

  • Chain 'M':
    No sequence available.

  • Chain 'N':
    Sequence, based on SEQRES records: (download) 
    >3cmaN (N:)
matgprykvpmrrrreartdyhqrlrllksgkprlvarksnkhvraqlvtlgpngddtla
sahssdlaeygweaptgnmpsayltgllaglraqeagveeavldiglnsptpgskvfaiq
egaidagldiphnddvladwqrtrgahiaeydeqleeplysgdfdaadlpehfdelretl
ldgdiel

    Sequence, based on observed residues (ATOM records): (download) 
    >3cmaN (N:)
atgprykvpmrrrreartdyhqrlrllksgkprlvarksnkhvraqlvtlgpngddtlas
ahssdlaeygweaptgnmpsayltgllaglraqeagveeavldiglnsptpgskvfaiqe
gaidagldiphnddvladwqrtrgahiaeydeqleeplysgdfdaadlpehfdelretll
dgdiel

  • Chain 'O':
    Sequence, based on SEQRES records: (download) 
    >3cmaO (O:)
msktnprlssliadlksaarssggavwgdvaerlekprrthaevnlgrieryaqedetvv
vpgkvlgsgvlqkdvtvaavdfsgtaetkidqvgeavsleqaiennpegshvrvir

    Sequence, based on observed residues (ATOM records): (download) 
    >3cmaO (O:)
sktnprlssliadlksaarssggavwgdvaerlekprrthaevnlgrieryaqedetvvv
pgkvlgsgvlqkdvtvaavdfsgtaetkidqvgeavsleqaiennpegshvrvir

  • Chain 'P':
    Sequence, based on SEQRES records: (download) 
    >3cmaP (P:)
mtdlsaqkrlaadvldvgknrvwfnperqgdiadaitredvrelvdegaiqakdkkgnsr
grarerqkkrayghqkgagsrkgkagarqnskedwesriraqrtklrelrdegtlsssqy
rdlydkagggefdsvadleryidanhgda

    Sequence, based on observed residues (ATOM records): (download) 
    >3cmaP (P:)
tdlsaqkrlaadvldvgknrvwfnperqgdiadaitredvrelvdegaiqakdkkgnsrg
rarerqkkrayghqkgagsrkgkagarqnskedwesriraqrtklrelrdegtlsssqyr
dlydkagggefdsvadleryida

  • Chain 'Q':
    Sequence, based on SEQRES records: (download) 
    >3cmaQ (Q:)
mpssngplegtrgklknkprdrgtsppqraveefddgekvhlkidpsvpngrfhprfdgq
tgtvegkqgdaykvdivdggkektiivtaahlrrqe

    Sequence, based on observed residues (ATOM records): (download) 
    >3cmaQ (Q:)
pssngplegtrgklknkprdrgtsppqraveefddgekvhlkidpsvpngrfhprfdgqt
gtvegkqgdaykvdivdggkektiivtaahlrrqe

  • Chain 'R':
    Sequence, based on SEQRES records: (download) 
    >3cmaR (R:)
mgisysveadpdttakamlrerqmsfkhskaiareikgktageavdyleaviegdqpvpf
kqhnsgvghkskvdgwdagrypekaskafldllenavgnadhqgfdgeamtikhvaahkv
geqqgrkpramgrasawnspqvdvelileepeved

    Sequence, based on observed residues (ATOM records): (download) 
    >3cmaR (R:)
gisysveadpdttakamlrerqmsfkhskaiareikgktageavdyleaviegdqpvpfk
qhnsgvghkskvdgwdagrypekaskafldllenavgnadhqgfdgeamtikhvaahkvg
eqqgrkpramgrasawnspqvdvelileep

  • Chain 'S':
    Sequence, based on SEQRES records: (download) 
    >3cmaS (S:)
mswdvikhphvtekamndmdfqnklqfavddraskgevadaveeqydvtveqvntqntmd
gekkavvrlsedddaqevasrigvf

    Sequence, based on observed residues (ATOM records): (download) 
    >3cmaS (S:)
swdvikhphvtekamndmdfqnklqfavddraskgevadaveeqydvtveqvntqntmdg
ekkavvrlsedddaqevasri

  • Chain 'T':
    Sequence, based on SEQRES records: (download) 
    >3cmaT (T:)
mskqpdkqrksqrraplherhkqvratlsadlreeygqrnvrvnagdtvevlrgdfagee
gevinvdldkavihvedvtlektdgeevprpldtsnvrvtdldledekrearleseddsa

    Sequence, based on observed residues (ATOM records): (download) 
    >3cmaT (T:)
skqpdkqrksqrraplherhkqvratlsadlreeygqrnvrvnagdtvevlrgdfageeg
evinvdldkavihvedvtlektdgeevprpldtsnvrvtdldledekrearleseddsa

  • Chain 'U':
    Sequence, based on SEQRES records: (download) 
    >3cmaU (U:)
mprtrecdycgtdiepgtgtmfvhkdgatthfcsskcennadlgrearnlewtdtargea
geaedea

    Sequence, based on observed residues (ATOM records): (download) 
    >3cmaU (U:)
recdycgtdiepgtgtmfvhkdgatthfcsskcennadlgrearnlewtdtar

  • Chain 'V':
    Sequence, based on SEQRES records: (download) 
    >3cmaV (V:)
mtvlhvqeirdmtpaereaelddlktellnaravqaaggapenpgrikelrkaiarikti
qgeegdlqene

    Sequence, based on observed residues (ATOM records): (download) 
    >3cmaV (V:)
tvlhvqeirdmtpaereaelddlktellnaravqaaggapenpgrikelrkaiariktiq
geegd

  • Chain 'W':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >3cmaW (W:)
mhalvqlrgevnmhtdiqdtlemlnihhvnhctlvpetdayrgmvakvndfvafgepsqe
tletvlatraeplegdadvddewvaehtdyddisglafallseettlreqglsptlrlhp
prgghdgvkhpvkeggqlgkhdtegiddlleamr

  • Chain 'X':
    Sequence, based on SEQRES records: (download) 
    >3cmaX (X:)
msasdfeervvtiplrdaraepnhkradkamilirehlakhfsvdedavrldpsineaaw
argrantpskirvraarfeeegeaiveaetae

    Sequence, based on observed residues (ATOM records): (download) 
    >3cmaX (X:)
ervvtiplrdaraepnhkradkamilirehlakhfsvdedavrldpsineaawargrant
pskirvraarfeeegeaiveae

  • Chain 'Y':
    Sequence, based on SEQRES records: (download) 
    >3cmaY (Y:)
madneedveaeeeyteltdisgvgpskaeslreagfesvedvrgadqsaladvsgignal
aarikadvggleveseteaeveeeggeeapdedvetelqargltektpdlsdedarlltq
rhrvgkpqfnrqdhhkkkrvstswrkprgqlskqrrgikgkgdtveagfrsptavrgkhp
sgfeevrvhnvddlegvdgdteavriaskvgarkrerieeeaedagirvlnptyvevevs

    Sequence, based on observed residues (ATOM records): (download) 
    >3cmaY (Y:)
telqargltektpdlsdedarlltqrhrvgkpqfnrqdhhkkkrvstswrkprgqlskqr
rgikgkgdtveagfrsptavrgkhpsgfeevrvhnvddlegvdgdteavriaskvgarkr
erieeeaedagirvlnptyvev

  • Chain 'Z':
    Sequence, based on SEQRES records: (download) 
    >3cmaZ (Z:)
msprarrepnleglmwplggqqttmasksgktgssgrfgarygrvsrrrvaeiesemned
hacpncgedrvdrqgtgiwqcsycdykftggsykpetpggktvrrsiraalsedee

    Sequence, based on observed residues (ATOM records): (download) 
    >3cmaZ (Z:)
ssgrfgarygrvsrrrvaeiesemnedhacpncgedrvdrqgtgiwqcsycdykftggsy
kpetpggktvrrs