Structure of PDB 5v8k Chain A Binding Site BS02

Receptor Information

>5v8k Chain A (length=600) Species: 35701 (Heliomicrobium modesticaldum)

NPRAQVFEYFKLKVPATRGAVLKAHINHLGNVAAMVSFILVHHLSWDPAT
QGVLWAPATMFYARLYQLGLDAVALSPDALFVARMHLLAAIILWGFGHVK
SPAEEKFLEKVTMGKALVAQFHFFALIATLWGLHMAFYGILGPSGKLEPT
GLSFDMFGPITPATMAGNHVAFGAVFFLGGIFHYFAGFNTKRFAFFEKDW
EAVLSVSCQILAFHFATVVFAMIIWQHPQLGFGFMREYAVSQYAGPELKM
IAQSNPGLLVKQAILGHLVMGIMFWIGGVFHGAHFMLRVLNDPKLAEEMK
DFKFIKRCYDHEFQKKFLALIMFGAFLPIFVSYGIATHNTIADIHAASKT
GLFAHMTYINIGTPLHDAIFGSKGSISEFVAAHAIAGGLHFTMVPMWRMV
FFSKVSPWTTKVGMKAKRDGEFPCLGPAYGGTCSISLVDQFYLAIFFSLQ
VIAPAWFYIDGCWMGSFVAVAAPYNDIYQAALATFNSHNPLHQLSPLTNM
GYFSYIIQQTTAMFSRYDGHMIQALLGAHFIWAFTFSMLFQYRGSRDEGA
MVLKWAHQQVGVGFAGKMYNRALSLKEGKAIGCFLFFKMTIVCMWALAMV

Ligand information

• Ligand ID: GB0
• InChI: InChI=1S/C50H59N4O5.Mg/c1-12-34-30(7)37-24-39-32(9)36(20-21-43(55)59-23-22-29(6)19-15-18-28(5)17-14-16-27(3)4)47(53-39)45-46(50(57)58-11)49(56)44-33(10)40(54-48(44)45)26-42-35(13-2)31(8)38(52-42)25-41(34)51-37;/h16,18,22,24-26,46H,12-15,17,19-21,23H2,1-11H3,(H-,51,52,53,54,56);/q-1;+2/p-1/b28-18+,29-22+,37-24-,38-25-,39-24-,40-26-,41-25-,42-26-,47-45-;/t46-;/m0./s1
• InChIKey: LRFAKGNZCOQNAG-QUMYBLOASA-M
• SMILES:
  OpenEye OEToolkits 2.0.6: CCc1c(c2n3c1C=C4C(=C5C(=O)[C@H](C6=C7C(=C(C8=CC9=[N]([Mg]3(N87)[N]4=C65)C(=C2)C(=C9C)CC)C)CCC(=O)OC/C=C(\C)/CC/C=C(\C)/CCC=C(C)C)C(=O)OC)C)C
  CACTVS 3.385: CCC1=C(C)C2=NC1=Cc3n4[Mg][N]5C(=C2)C(=C(CCC(=O)OCC=C(C)CCC=C(C)CCC=C(C)C)C5=C6[CH](C(=O)OC)C(=O)C7=C(C)C(=Cc4c(CC)c3C)N=C67)C
  ACDLabs 12.01: C(\C=C(/C)CC\C=C(\CC\C=C(/C)C)C)OC(CCC=4C5=C2C1=N7C(C(=C1C(C2C(=O)OC)=O)C)=Cc9c(c(c8C=C3N6=C(C(=C3CC)C)C=C(C=4C)N5[Mg]67n89)C)CC)=O
  OpenEye OEToolkits 2.0.6: CCc1c(c2n3c1C=C4C(=C5C(=O)C(C6=C7C(=C(C8=CC9=[N]([Mg]3(N87)[N]4=C65)C(=C2)C(=C9C)CC)C)CCC(=O)OCC=C(C)CCC=C(C)CCC=C(C)C)C(=O)OC)C)C
  CACTVS 3.385: CCC1=C(C)C2=NC1=Cc3n4[Mg][N@@]5C(=C2)C(=C(CCC(=O)OC\C=C(/C)CC\C=C(C)\CCC=C(C)C)C5=C6[C@H](C(=O)OC)C(=O)C7=C(C)C(=Cc4c(CC)c3C)N=C67)C
• Formula: C50 H58 Mg N4 O5
• Name: Bacteriochlorophyll g'
• PDB chain: 5v8k Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5v8k Structure of a symmetric photosynthetic reaction center-photosystem.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): Y341 F465 M472 F475 Y510 I514 T518 H537 W540 T598 C601 M602 L605
• Binding residue (residue number reindexed from 1): Y333 F457 M464 F467 Y502 I506 T510 H529 W532 T590 C593 M594 L597
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0015979 photosynthesis

Cellular Component

• GO:0009579 thylakoid
• GO:0016020 membrane

External links

• PDB: RCSB:5v8k, PDBe:5v8k, PDBj:5v8k
• PDBsum: 5v8k
• PubMed: 28751471
• UniProt: Q1MX24