PDB entry 1nji

View 1nji on RCSB PDB site
Description: Structure of chloramphenicol bound to the 50S ribosomal subunit
Class: ribosome
Keywords: 50S, antibiotic, chloramphenicol, LSU, RIBOSOME
Deposited on 2002-12-31, released 2003-07-22
The last revision prior to the SCOPe 2.08 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 3 Å
R-factor: 0.176
AEROSPACI score: 0.27 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '1':
    Compound: 50S ribosomal protein L37Ae
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed):
    • PDB 1NJI (0-72)
    Domains in SCOPe 2.08: d1nji1_
  • Chain '2':
    Compound: 50S ribosomal protein L37e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1nji2_
  • Chain '3':
    Compound: 50S ribosomal protein L39e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1nji3_
  • Chain '4':
    Compound: 50S ribosomal protein L44E
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1nji4_
  • Chain 'A':
    Compound: 23S ribosomal RNA
    Species: Haloarcula marismortui [TaxId:2238]
  • Chain 'B':
    Compound: 5S ribosomal RNA
    Species: Haloarcula marismortui [TaxId:2238]
  • Chain 'C':
    Compound: 50S ribosomal protein L2P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njic1, d1njic2
  • Chain 'D':
    Compound: 50S ribosomal protein L3P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P20279 (0-336)
      • see remark 999 (309)
    Domains in SCOPe 2.08: d1njid_
  • Chain 'E':
    Compound: 50S ribosomal protein L4E
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njie_
  • Chain 'F':
    Compound: 50S ribosomal protein L5P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njif_
  • Chain 'G':
    Compound: 50S ribosomal protein L6P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njig1, d1njig2
  • Chain 'H':
    Compound: 50S ribosomal protein L7Ae
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njih_
  • Chain 'I':
    Compound: Acidic ribosomal protein P0 homolog
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njii_
  • Chain 'J':
    Compound: 50S ribosomal protein L10e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed):
    • PDB 1NJI (0-166)
    Domains in SCOPe 2.08: d1njij_
  • Chain 'K':
    Compound: 50S ribosomal protein L13P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njik_
  • Chain 'L':
    Compound: 50S ribosomal protein L14P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njil_
  • Chain 'M':
    Compound: 50S ribosomal protein L15P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njim_
  • Chain 'N':
    Compound: 50S ribosomal protein L15e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed):
    • PDB 1NJI (0-193)
    Domains in SCOPe 2.08: d1njin_
  • Chain 'O':
    Compound: 50S ribosomal protein L18P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njio_
  • Chain 'P':
    Compound: 50S ribosomal protein L18e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njip_
  • Chain 'Q':
    Compound: 50S ribosomal protein L19e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njiq_
  • Chain 'R':
    Compound: 50S ribosomal protein L21e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njir_
  • Chain 'S':
    Compound: 50S ribosomal protein L22P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njis_
  • Chain 'T':
    Compound: 50S ribosomal protein L23P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njit_
  • Chain 'U':
    Compound: 50S ribosomal protein L24P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njiu_
  • Chain 'V':
    Compound: 50S ribosomal protein L24e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njiv_
  • Chain 'W':
    Compound: 50S ribosomal protein L29P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njiw_
  • Chain 'X':
    Compound: 50S ribosomal protein L30P
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njix_
  • Chain 'Y':
    Compound: 50S ribosomal protein L31e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njiy_
  • Chain 'Z':
    Compound: 50S ribosomal protein L32e
    Species: Haloarcula marismortui [TaxId:2238]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d1njiz_
  • Heterogens: MG, K, NA, CL, CLM, CD, HOH

PDB Chain Sequences:

  • Chain '1':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1nji1 (1:)
rtgrfgpryglkirvrvadveikhkkkhkcpvcgfkklkragtgiwmcghcgykiaggcy
qpetvagkavmka

  • Chain '2':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1nji2 (2:)
tgagtpsqgkknttthtkcrrcgeksyhtkkkvcsscgfgksakrrdyewqskage

  • Chain '3':
    Sequence, based on SEQRES records: (download) 
    >1nji3 (3:)
gkkskatkkrlakldnqnsrvpawvmlktdevqrnhkrrhwrrndtde

    Sequence, based on observed residues (ATOM records): (download) 
    >1nji3 (3:)
gkkskatkkrlakldnqnsrvpawvmlktdernhkrrhwrrndtde

  • Chain '4':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1nji4 (4:)
mqmprrfntycphcnehqehevekvrsgrqtgmkwidrqrernsgigndgkfskvpggdk
ptkktdlkyrcgecgkahlregwragrlefqe

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >1njiC (C:)
grriqgqrrgrgtstfrapshrykadlehrkvedgdviagtvvdiehdparsapvaavef
edgdrrlilapegvgvgdelqvgvdaeiapgntlplaeipegvpvcnvesspgdggkfar
asgvnaqllthdrnvavvklpsgemkrldpqcratigvvggggrtdkpfvkagnkhhkmk
argtkwpnvrgvamnavdhpfggggrqhpgkpksisrnappgrkvgdiaskrtgrggne

    Sequence, based on observed residues (ATOM records): (download) 
    >1njiC (C:)
grriqgqrrgrgtstfrapshrykadlehrkvedgdviagtvvdiehdparsapvaavef
edgdrrlilapegvgvgdelqvgvdaeiapgntlplaeipegvpvcnvesspgdggkfar
asgvnaqllthdrnvavvklpsgemkrldpqcratigvvggggrtdkpfvkagnkhhkmk
argtkwpnvrgvamnavdhpfggggrqhpgkpksisrnappgrkvgdiaskrtgrgg

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1njiD (D:)
pqpsrprkgslgfgprkrstsetprfnswpsddgqpgvqgfagykagmthvvlvndepns
pregmeetvpvtvietppmravalrayedtpygqrpltevwtdefhseldrtldvpedhd
pdaaeeqirdaheagdlgdlrlithtvpdavpsvpkkkpdvmetrvgggsvsdrldhald
ivedggehamndifrageyadvagvtkgkgtqgpvkrwgvqkrkgkharqgwrrrignlg
pwnpsrvrstvpqqgqtgyhqrtelnkrlidigegdeptvdggfvnygevdgpytlvkgs
vpgpdkrlvrfrpavrpndqprldpevryvsnesnqg

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1njiE (E:)
mqatiydldgntdgevdlpdvfetpvrsdligkavraaqanrkqdygsdeyaglrtpaes
fgsgrgqahvpkldgrarrvpqavkgrsahppktekdrsldlndkerqlavrsalaatad
adlvadrghefdrdevpvvvsddfedlvktqevvsllealdvhadidradetkikagqgs
argrkyrrpasilfvtsdepstaarnlagadvatasevntedlapggapgrltvftesal
aevaer

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >1njiF (F:)
ssesesggdfhemrepriekvvvhmgighggrdlanaedilgeitgqmpvrtkakrtvge
fdiregdpigakvtlrdemaeeflqtalplaelatsqfddtgnfsfgveehtefpsqeyd
psigiygldvtvnlvrpgyrvakrdkasrsiptkhrlnpadavafiestydvevse

    Sequence, based on observed residues (ATOM records): (download) 
    >1njiF (F:)
fhemrepriekvvvhmgighanaedilgeitgqmpvrtkakrtvgefdiregdpigakvt
lrdemaeeflqtalplaelatsqfddtgnfsfgldvtvnlvrpgyrvakrdkasrsiptk
hrlnpadavafiestydvev

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >1njiG (G:)
prveleipedvdaeqdhlditvegdngsvtrrlwypdidvsvdgdtvviesdednaktms
tigtfqshienmfhgvtegweygmevfyshfpmqvnvegdevvienflgekaprrttihg
dtdveidgeeltvsgpdieavgqtaadieqltrindkdvrvfqdgvyitrkpnrgda

    Sequence, based on observed residues (ATOM records): (download) 
    >1njiG (G:)
prveleipedvdaeqdhlditvegdngsvtrrlwypdidvsvdgdtvviesdednaktms
tigtfqshienmfhgvtegweygmevfyshfpmqvnvegdevvienflgekaprrttihg
dtdveidgeeltvsgpdieavgqtaadieqltrindkdvrvfqdgvyitrkp

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1njiH (H:)
pvyvdfdvpadleddalealevardtgavkkgtnettksiergsaelvfvaedvqpeeiv
mhipeladekgvpfifveqqddlghaaglevgsaaaavtdagaaatvleeiadkveelr

  • Chain 'I':
    Sequence, based on SEQRES records: (download) 
    >1njiI (I:)
msaeserktetipewkqeevdaivemiesyesvgvvniagipsrqlqdmrrdlhgtaelr
vsrntlleralddvddgledlngyitgqvgligtddnpfslfqeleasktpapigageva
pndivipegdtgvdpgpfvgelqsvgadariqegsiqvlsdstvldtgeevsqelsnvln
elgiepkevgldlravfadgvlfepeeleldideyrsdiqaaagrafnlsvnadyptatt
aptmlqsdrgnakslalqaaiedpevvpdlvskadaqvralasqiddeealpeelqgvea
dvateeptddqdddtaseddadaddaaeeadddddddedagdalgamf

    Sequence, based on observed residues (ATOM records): (download) 
    >1njiI (I:)
ipewkqeevdaivemiesrntlleraldd

  • Chain 'J':
    Sequence, based on SEQRES records: (download) 
    >1njiJ (J:)
kpgamyrnsskpaytrreyisgipgkkiaqfdmgnngagptypaqvelvvekpvqirhna
leaarvaanryvqnsgaaanykfrirkfpfhvirenkaaaaaaaaaaadgmrapfgkpvg
taarvhganhifiawvnpdpnveeawrrakmkvtptinidsspagna

    Sequence, based on observed residues (ATOM records): (download) 
    >1njiJ (J:)
kpgamyrnsskpaytrreyisgipgkkiaqfdmgnngagptypaqvelvvekpvqirhna
leaarvaanryvqnsgaaanykfrirkfpfhvirenkdgmrapfgkpvgtaarvhganhi
fiawvnpdpnveeawrrakmkvtptinidsspagna

  • Chain 'K':
    Sequence, based on SEQRES records: (download) 
    >1njiK (K:)
msvaefdadvivdardcimgrvasqvaeqaldgetvavvnaeravitgreeqivekyekr
vdigndngyfypkrpdgifkrtirgmlphkkqrgreafesvrvylgnpydedgevldgts
ldrlsnikfvtlgeisetlganktw

    Sequence, based on observed residues (ATOM records): (download) 
    >1njiK (K:)
aefdadvivdardcimgrvasqvaeqaldgetvavvnaeravitgreeqivekyekrvdi
gndngyfypkrpdgifkrtirgmlphkkqrgreafesvrvylgnpydedgevldgtsldr
lsnikfvtlgeisetlganktw

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1njiL (L:)
mealgadvtqglekgslitcadntgarelkvisvhgysgtknrhpkaglgdkitvsvtkg
tpemrrqvleavvvrqrkpirrpdgtrvkfednaavivdenedprgtelkgpiarevaqr
fgsvasaatmiv

  • Chain 'M':
    Sequence, based on SEQRES records: (download) 
    >1njiM (M:)
tskkkrqrgsrthgggshknrrgaghrggrgdagrdkhefhnheplgksgfkrpqkvqee
aatidvreidenvtllaaddvaevedggfrvdvrdvveeaddadyvkvlgagqvrheltl
iaddfsegarekvegaggsveltdlgeerqaeaeetedadadee

    Sequence, based on observed residues (ATOM records): (download) 
    >1njiM (M:)
tskkkrqrgsrthgggshknrrgaghrggrgdagrdkhefhnheplgksgfkrpqkvqee
aatidvreidenvtllaaddvaefrvdvrdvveeaddadyvkvlgagqvrheltliaddf
segarekvegaggsveltdlgeerq

  • Chain 'N':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1njiN (N:)
arsaysyireawkrpkegqiaelmwhrmqewrnepavvrierptrldrarslgykakqgi
ivvrvairkgssrrtrfnkgrrskrmmvnritrkkniqriaeeranrkfpnlrvlnsysv
gedgrhkwhevilidpdhpaiksddqlswisrtrhrlrtfrgltsagrrcrglrgqgkgs
ekvrpslrvngaka

  • Chain 'O':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1njiO (O:)
atgprykvpmrrrreartdyhqrlrllksgkprlvarksnkhvraqlvtlgpngddtlas
ahssdlaeygweaptgnmpsayltgllaglraqeagveeavldiglnsptpgskvfaiqe
gaidagldiphnddvladwqrtrgahiaeydeqleeplysgdfdaadlpehfdelretll
dgdiel

  • Chain 'P':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1njiP (P:)
sktnprlssliadlksaarssggavwgdvaerlekprrthaevnlgrieryaqedetvvv
pgkvlgsgvlqkdvtvaavdfsgtaetkidqvgeavsleqaiennpegshvrvir

  • Chain 'Q':
    Sequence, based on SEQRES records: (download) 
    >1njiQ (Q:)
tdlsaqkrlaadvldvgknrvwfnperqgdiadaitredvrelvdegaiqakdkkgnsrg
rarerqkkrakghqkgagsrkgkagarqnskedwesriraqrtklrelrdegtlsssqyr
dlydkagggefdsvadleryidanhgda

    Sequence, based on observed residues (ATOM records): (download) 
    >1njiQ (Q:)
tdlsaqkrlaadvldvgknrvwfnperqgdiadaitredvrelvdegaiqakdkkgnsrg
rarerqkkrakghqkgagsrkgkagarqnskedwesriraqrtklrelrdegtlsssqyr
dlydkagggefdsvadleryida

  • Chain 'R':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1njiR (R:)
pssngplegtrgklknkprdrgtsppqraveefddgekvhlkidpsvpngrfhprfdgqt
gtvegkqgdaykvdivdggkektiivtaahlrrqe

  • Chain 'S':
    Sequence, based on SEQRES records: (download) 
    >1njiS (S:)
gisysveadpdttakamlrerqmsfkhskaiareikgktageavdyleaviegdqpvpfk
qhnsgvghkskvdgwdagrypekaskafldllenavgnadhqgfdgeamtikhvaahkvg
eqqgrkpramgrasawnspqvdvelileepeved

    Sequence, based on observed residues (ATOM records): (download) 
    >1njiS (S:)
gisysveadpdttakamlrerqmsfkhskaiareikgktageavdyleaviegdqpvpfk
qhnsgvghkskvdgwdagrypekaskafldllenavgnadhqgfdgeamtikhvaahkvg
eqqgrkpramgrasawnspqvdvelileep

  • Chain 'T':
    Sequence, based on SEQRES records: (download) 
    >1njiT (T:)
swdvikhphvtekamndmdfqnklqfavddraskgevadaveeqydvtveqvntqntmdg
ekkavvrlsedddaqevasrigvf

    Sequence, based on observed residues (ATOM records): (download) 
    >1njiT (T:)
swdvikhphvtekamndmdfqnklqfavddraskgevadaveeqydvtveqvntqntmdg
ekkavvrlsedddaqevasri

  • Chain 'U':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1njiU (U:)
skqpdkqrksqrraplherhkqvratlsadlreeygqrnvrvnagdtvevlrgdfageeg
evinvdldkavihvedvtlektdgeevprpldtsnvrvtdldledekrearleseddsa

  • Chain 'V':
    Sequence, based on SEQRES records: (download) 
    >1njiV (V:)
prtrecdycgtdiepgtgtmfvhkdgatthfcsskcennadlgrearnlewtdtargeag
eaedea

    Sequence, based on observed residues (ATOM records): (download) 
    >1njiV (V:)
recdycgtdiepgtgtmfvhkdgatthfcsskcennadlgrearnlewtdtar

  • Chain 'W':
    Sequence, based on SEQRES records: (download) 
    >1njiW (W:)
tvlhvqeirdmtpaereaelddlktellnaravqaaggapenpgrikelrkaiariktiq
geegdlqene

    Sequence, based on observed residues (ATOM records): (download) 
    >1njiW (W:)
tvlhvqeirdmtpaereaelddlktellnaravqaaggapenpgrikelrkaiariktiq
geegd

  • Chain 'X':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >1njiX (X:)
mhalvqlrgevnmhtdiqdtlemlnihhvnhctlvpetdayrgmvakvndfvafgepsqe
tletvlatraeplegdadvddewvaehtdyddisglafallseettlreqglsptlrlhp
prgghdgvkhpvkeggqlgkhdtegiddlleamr

  • Chain 'Y':
    Sequence, based on SEQRES records: (download) 
    >1njiY (Y:)
sasdfeervvtiplrdaraepnhkradkamilirehlakhfsvdedavrldpsineaawa
rgrantpskirvraarfeeegeaiveaetae

    Sequence, based on observed residues (ATOM records): (download) 
    >1njiY (Y:)
ervvtiplrdaraepnhkradkamilirehlakhfsvdedavrldpsineaawargrant
pskirvraarfeeegeaiveae

  • Chain 'Z':
    Sequence, based on SEQRES records: (download) 
    >1njiZ (Z:)
adneedveaeeeyteltdisgvgpskaeslreagfesvedvrgadqsaladvsgignala
arikadvggleveseteaeveeeggeeapdedvetelqargltektpdlsdedarlltqr
hrvgkpqfnrqdhhkkkrvstswrkprgqlskqrrgikgkgdtveagfrsptavrgkhps
gfeevrvhnvddlegvdgdteavriaskvgarkrerieeeaedagirvlnptyvevevse

    Sequence, based on observed residues (ATOM records): (download) 
    >1njiZ (Z:)
telqargltektpdlsdedarlltqrhrvgkpqfnrqdhhkkkrvstswrkprgqlskqr
rgikgkgdtveagfrsptavrgkhpsgfeevrvhnvddlegvdgdteavriaskvgarkr
erieeeaedagirvlnptyvev