PDB entry 7dkz

View 7dkz on RCSB PDB site
Description: Structure of plant photosystem I-light harvesting complex I supercomplex
Class: photosynthesis
Keywords: PSI-LHCI high plants, PHOTOSYNTHESIS
Deposited on 2020-11-25, released 2021-03-31
The last revision prior to the SCOPe 2.08 freeze date was dated 2021-07-21, with a file datestamp of 2021-07-16.
Experiment type: XRAY
Resolution: 2.39 Å
R-factor: N/A
AEROSPACI score: 0.29 (click here for full SPACI score report)

Chains and heterogens:

  • Chain '1':
    Compound: Lhca1
    Species: Pisum sativum [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • PDB 7DKZ (0-194)
    Domains in SCOPe 2.08: d7dkz1_
  • Chain '2':
    Compound: Chlorophyll a-b binding protein, chloroplastic
    Species: PISUM SATIVUM [TaxId:3888]
    Gene: lhaB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d7dkz2_
  • Chain '3':
    Compound: Chlorophyll a-b binding protein 3, chloroplastic
    Species: PISUM SATIVUM [TaxId:3888]
    Gene: lhca3
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d7dkz3_
  • Chain '4':
    Compound: chlorophyll a-b binding protein p4, chloroplastic
    Species: PISUM SATIVUM [TaxId:3888]
    Gene: lhcA-P4
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9SQL2 (0-197)
      • conflict (37)
      • conflict (76)
      • conflict (97)
    Domains in SCOPe 2.08: d7dkz4_
  • Chain 'A':
    Compound: photosystem I p700 chlorophyll a apoprotein a1
    Species: PISUM SATIVUM [TaxId:3888]
    Gene: psaA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d7dkza_
  • Chain 'B':
    Compound: photosystem I p700 chlorophyll a apoprotein a2
    Species: PISUM SATIVUM [TaxId:3888]
    Gene: psaB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d7dkzb_
  • Chain 'C':
    Compound: photosystem I iron-sulfur center
    Species: PISUM SATIVUM [TaxId:3888]
    Gene: psaC, frxA
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d7dkzc_
  • Chain 'D':
    Compound: PsaD
    Species: Pisum sativum [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • PDB 7DKZ (0-142)
    Domains in SCOPe 2.08: d7dkzd_
  • Chain 'E':
    Compound: PsaE
    Species: PISUM SATIVUM [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • Uniprot E1C9K6 (2-60)
      • expression tag (0-1)
      • conflict (15)
      • expression tag (61-65)
    Domains in SCOPe 2.08: d7dkze1, d7dkze2
  • Chain 'F':
    Compound: psi-f
    Species: PISUM SATIVUM [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • Uniprot A0A0M3KL12 (0-153)
      • conflict (2)
      • conflict (9)
      • conflict (30)
      • conflict (33)
      • conflict (56)
      • conflict (110)
      • conflict (126)
    Domains in SCOPe 2.08: d7dkzf_
  • Chain 'G':
    Compound: PsaG
    Species: Pisum sativum [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • PDB 7DKZ (0-96)
  • Chain 'H':
    Compound: PsaH
    Species: Pisum sativum [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • PDB 7DKZ (0-87)
  • Chain 'I':
    Compound: Photosystem I reaction center subunit VIII
    Species: PISUM SATIVUM [TaxId:3888]
    Gene: PSAI
    Database cross-references and differences (RAF-indexed):
  • Chain 'J':
    Compound: Photosystem I reaction center subunit IX
    Species: PISUM SATIVUM [TaxId:3888]
    Gene: psaJ
    Database cross-references and differences (RAF-indexed):
    • Uniprot D5MAL3 (0-41)
      • conflict (31)
    Domains in SCOPe 2.08: d7dkzj_
  • Chain 'K':
    Compound: psi-k
    Species: PISUM SATIVUM [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • Uniprot E1C9L3 (0-79)
      • conflict (39)
  • Chain 'L':
    Compound: PsaL
    Species: Pisum sativum [TaxId:3888]
    Database cross-references and differences (RAF-indexed):
    • PDB 7DKZ (0-156)
    Domains in SCOPe 2.08: d7dkzl_
  • Heterogens: DGD, LHG, LMG, CLA, CHL, LUT, XAT, BCR, LMT, HTG, PQN, SF4, HOH

PDB Chain Sequences:

  • Chain '1':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >7dkz1 (1:)
adwmpgqprpsyldgsapgdfgfdplrlgevpenlerfkeselihcrwamlavpgilvpe
alglgnwvkaqewaalpggqatylgnpvpwgtlptilvieflsiafvehqrsmekdpekk
kypggafdplgyskdpkkfheykikevkngrlallafvgicvqqsaypgtgplenlathl
adpwhntignvlipa

  • Chain '2':
    Sequence, based on SEQRES records: (download) 
    >7dkz2 (2:)
masacassaiaavaistpssqkngspsgtskaflgrklkvnsstaspsrvrststvctva
epdrplwfpgstpppwldgslpgdfgfdplglgsdpeslrwnvqaelvhsrwamlgaagi
fipefltklgilntpswytageqeyftdtttlfivelvfigwaegrrwadilnpgcvntd
pifpnnkltgtdvgypgglwfdplgwgsaspqklkelrtkeikngrlamlavmgawfqhi
ytgtgpidnlfahladpghatifaaftpk

    Sequence, based on observed residues (ATOM records): (download) 
    >7dkz2 (2:)
pdrplwfpgstpppwldgslpgdfgfdplglgsdpeslrwnvqaelvhsrwamlgaagif
ipefltklgilntpswytageqeyftdtttlfivelvfigwaegrrwadilnpgcvntdp
ifpnnkltgtdvgypgglwfdplgwgsaspqklkelrtkeikngrlamlavmgawfqhiy
tgtgpidnlfahladpghatifaa

  • Chain '3':
    Sequence, based on SEQRES records: (download) 
    >7dkz3 (3:)
matqalvssssltfaaeavrqsfrarslpssvgcsrkglvraaatppvkqggvdrplwfa
skqslsyldgslpgdygfdplglsdpegtggfieprwlaygevingrfamlgavgaiape
ylgkvglipqetalawfqtgvippagtynywadnytlfvlemalmgfaehrrfqdwakpg
smgkqyflglekgfggsgnpaypggpffnplgfgkdekslkelklkevkngrlamlailg
yfiqglvtgvgpyqnlldhvadpvnnnvltslkfh

    Sequence, based on observed residues (ATOM records): (download) 
    >7dkz3 (3:)
plwfaskqslsyldgslpgdygfdplglsdpegtggfieprwlaygevingrfamlgavg
aiapeylgkvglipqetalawfqtgvippagtynywadnytlfvlemalmgfaehrrfqd
wakpgsmgkqyflglekgfggsgnpaypggpffnplgfgkdekslkelklkevkngrlam
lailgyfiqglvtgvgpyqnlldhvadpvnnnvlts

  • Chain '4':
    Sequence, based on SEQRES records: (download) 
    >7dkz4 (4:)
kkgewlpglaspgyltgslpgdngfdplglaedpenlkwfvqaelvngrwamlgvagmll
pevftsigiinvpkwydagkeeyfassstlfviefilfhyveirrwqdiknpgsvnqdpi
fkqyslpagevgypggifnplnfaptleakekeiangrlamlaflgfiiqhnvtgkgpfd
nllqhisdpwhntivqtl

    Sequence, based on observed residues (ATOM records): (download) 
    >7dkz4 (4:)
kgewlpglaspgyltgslpgdngfdplglaedpenlkwfvqaelvngrwamlgvagmllp
evftsigiinvpkwydagkeeyfassstlfviefilfhyveirrwqdiknpgsvnqdpif
kqyslpagevgypggifnplnfaptleakekeiangrlamlaflgfiiqhnvtgkgpfdn
llqhisdpwhntivq

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >7dkzA (A:)
miirspepkvqiladpevkilvdrdpiktsfeqwakpghfsrtiakgpdtttwiwnlhad
ahdfdshtsdleeisrkvfsahfgqlsiiflwlsgmyfhgarfsnyeawlndpthirpsa
qvvwpivgqeilngdvgggfrgiqitsgffqiwrasgitselqlyctaigalvfaalmlf
agwfhyhkaapklvwfqdvesmlnhhlagllglgslswaghqihvslpinqflnagvdpk
eiplphefilnrdllaqlypsfaegatpfftlnwskyadfltfrggldpltgglwltdia
hhhlaiailfliaghmyrtnwgighgikdileahkgpftgqghkglyeilttswhaqlsi
nlamlgsltiivahhmyamppypylatdygtqlslfthhmwiggflivgaaahaaifmvr
dydpttryndlldrvlrhrdaiishlnwvciflgfhsfglyihndtmsalgrpqdmfsdt
aiqlqpvfaqwiqnthalapgttapgattstsltwgggdlvsvggkvallpiplgtadfl
vhhihaftihvtvlillkgvlfarssrlipdkanlgfrfpcdgpgrggtcqvsawdhvfl
glfwmynaisvvifhfswkmqsdvwgsindqgvvthitggnfaqssitingwlrdflwaq
asqviqsygsslsayglfflgahfvwafslmflfsgrgywqeliesivwahnklkvapat
qpralsivqgravgvthyllggiattwafflariiavg

    Sequence, based on observed residues (ATOM records): (download) 
    >7dkzA (A:)
evkilvdrdpiktsfeqwakpghfsrtiakgpdtttwiwnlhadahdfdshtsdleeisr
kvfsahfgqlsiiflwlsgmyfhgarfsnyeawlndpthirpsaqvvwpivgqeilngdv
gggfrgiqitsgffqiwrasgitselqlyctaigalvfaalmlfagwfhyhkaapklvwf
qdvesmlnhhlagllglgslswaghqihvslpinqflnagvdpkeiplphefilnrdlla
qlypsfaegatpfftlnwskyadfltfrggldpltgglwltdiahhhlaiailfliaghm
yrtnwgighgikdileahkgpftgqghkglyeilttswhaqlsinlamlgsltiivahhm
yamppypylatdygtqlslfthhmwiggflivgaaahaaifmvrdydpttryndlldrvl
rhrdaiishlnwvciflgfhsfglyihndtmsalgrpqdmfsdtaiqlqpvfaqwiqnth
alapgttapgattstsltwgggdlvsvggkvallpiplgtadflvhhihaftihvtvlil
lkgvlfarssrlipdkanlgfrfpcdgpgrggtcqvsawdhvflglfwmynaisvvifhf
swkmqsdvwgsindqgvvthitggnfaqssitingwlrdflwaqasqviqsygsslsayg
lfflgahfvwafslmflfsgrgywqeliesivwahnklkvapatqpralsivqgravgvt
hyllggiattwafflariiavg

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >7dkzB (B:)
malrfprfsqglaqdpttrriwfgiatahdfeshdditegrlyqnifashfgqlaiiflw
tsgnlfhvawqgnfeawvqdplhvrpiahaiwdphfgqpaveaftrggalgpvniaysgv
yqwwytiglrtnedlytgaifllflsfisllagwlhlqpkwkpsvswfknaesrlnhhls
glfgvsslawaghlvhvaipgsrgeyvrwnnflsvlphpqglgplftgqwnlyaqnpdss
nhlfstsqgagtailtllggfhpqtqslwltdmahhhlaiailfligghmyrtnfgighs
ikyileahippggrlgrghkglydtinnsihfqlglalaslgvitslvaqhmyslpayaf
iaqdfttqaalythhqyiagfimtgafahgaiffirdynpeqnadnvlarmlehkeaiis
hlswaslflgfhtlglyvhndvmlafgtpekqiliepifaqwiqsahgktsygfdvllss
tnspalnagrsiwlpgwlnainensnslfltigpgdflvhhaialglhtttlilvkgald
argsklmpdkkdfgysfpcdgpgrggtcdisawdafylavfwmlntigwvtfywhwkhit
lwqgnvsqfnesstylmgwlrdylwlnssqlingynpfgmnslsvwawmflfghlvwatg
fmfliswrgywqelietlawahertplanlirwrdkpvalsivqarlvglvhfsvgyift
yaafliastsgkfg

    Sequence, based on observed residues (ATOM records): (download) 
    >7dkzB (B:)
alrfprfsqglaqdpttrriwfgiatahdfeshdditegrlyqnifashfgqlaiiflwt
sgnlfhvawqgnfeawvqdplhvrpiahaiwdphfgqpaveaftrggalgpvniaysgvy
qwwytiglrtnedlytgaifllflsfisllagwlhlqpkwkpsvswfknaesrlnhhlsg
lfgvsslawaghlvhvaipgsrgeyvrwnnflsvlphpqglgplftgqwnlyaqnpdssn
hlfstsqgagtailtllggfhpqtqslwltdmahhhlaiailfligghmyrtnfgighsi
kyileahippggrlgrghkglydtinnsihfqlglalaslgvitslvaqhmyslpayafi
aqdfttqaalythhqyiagfimtgafahgaiffirdynpeqnadnvlarmlehkeaiish
lswaslflgfhtlglyvhndvmlafgtpekqiliepifaqwiqsahgktsygfdvllsst
nspalnagrsiwlpgwlnainensnslfltigpgdflvhhaialglhtttlilvkgalda
rgsklmpdkkdfgysfpcdgpgrggtcdisawdafylavfwmlntigwvtfywhwkhitl
wqgnvsqfnesstylmgwlrdylwlnssqlingynpfgmnslsvwawmflfghlvwatgf
mfliswrgywqelietlawahertplanlirwrdkpvalsivqarlvglvhfsvgyifty
aafliastsgkfg

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >7dkzC (C:)
mshsvkiydtcigctqcvracptdvlemipwggckakqiasaprtedcvgckrcesacpt
dflsvrvylwhettrsmglay

    Sequence, based on observed residues (ATOM records): (download) 
    >7dkzC (C:)
shsvkiydtcigctqcvracptdvlemipwggckakqiasaprtedcvgckrcesacptd
flsvrvylwhettrsmglay

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >7dkzD (D:)
gftppeldpntpspifggstggllrkaqveefyvitwespkeqifemptggaaimregpn
llklarkeqclalgtrlrskykikyqfyrvfpsgevqylhpkdgvypekvnpgrqgvgvn
frsigknvspievkftgkqpydl

    Sequence, based on observed residues (ATOM records): (download) 
    >7dkzD (D:)
ppeldpntpspifggstggllrkaqveefyvitwespkeqifemptggaaimregpnllk
larkeqclalgtrlrskykikyqfyrvfpsgevqylhpkdgvypekvnpgrqgvgvnfrs
igknvspievkftgkqpydl

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >7dkzE (E:)
ppigpkrgakvkilrqesywykgtgsvvavdqdpntrypvvvrfnkvnyanvstnnyald
eveevk

    Sequence, based on observed residues (ATOM records): (download) 
    >7dkzE (E:)
igpkrgakvkilrqesywykgtgsvvavdqdpntrypvvvrfnkvnyanvstnnyaldev
eev

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >7dkzF (F:)
diagltpckdskqfakrekqsikklesslklyapdsapalainatiektkrrfdnygkqg
llcgadglphlivsgdqrhwgefitpgilflyiagwigwvgrsyliairddkkptqkeii
idvplatrlvfrgfswpiaayrellngelvakdv

    Sequence, based on observed residues (ATOM records): (download) 
    >7dkzF (F:)
diagltpckdskqfakrekqsikklesslklyapdsapalainatiektkrrfdnygkqg
llcgadglphlivsgdqrhwgefitpgilflyiagwigwvgrsyliairddkkptqkeii
idvplatrlvfrgfswpiaayrellngelvak

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    Sequence, based on SEQRES records: (download) 
    >7dkzJ (J:)
mrdlktylsvapvastlwfaalagllieinrffpdaltfpff

    Sequence, based on observed residues (ATOM records): (download) 
    >7dkzJ (J:)
mrdlktylsvapvastlwfaalagllieinrffpdaltf

  • Chain 'K':
    No sequence available.

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >7dkzL (L:)
yqvvqpingdpfigsletpvtssplvawylsnlpgyrtavnpllrgievglahgfllvgp
fvkagplrnteiagqagslaagglvvilsicltiygissfnegdpstapsltltgrkkqp
dqlqtadgwakftggfffggisgviwaffllyvldlp

    Sequence, based on observed residues (ATOM records): (download) 
    >7dkzL (L:)
vvqpingdpfigsletpvtssplvawylsnlpgyrtavnpllrgievglahgfllvgpfv
kagplrnteiagqagslaagglvvilsicltiygissfnegdpstapsltltgrkkqpdq
lqtadgwakftggfffggisgviwaffllyv