Structure of PDB 3gyx Chain K Binding Site BS01

Receptor Information

>3gyx Chain K (length=662) Species: 879 (Megalodesulfovibrio gigas)

KIPSKETPRGVAIAEPIIVEHSVDLLMVGGGMGNCGAAFEAVRWADKYAP
EAKILLVDKASLERSGAVAQGLSAINTYLGDNNADDYVRMVRTDLMGLVR
EDLIYDLGRHVDDSVHLFEEWGLPVWIKDEHGHNLDGAQAKAAGKSLRNG
DKPVRSGRWQIMINGESYKVIVAEAAKNALGQDRIIERIFIVKLLLDKNT
PNRIAGAVGFNLRANEVHIFKANAMVVACGGAVNVYRPRSVGEGMGRAWY
PVWNAGSTYTMCAQVGAEMTMMENRFVPARFKDGYGPVGAWFLLFKAKAT
NCKGEDYCATNRAMLKPYEERGYAKGHVIPTCLRNHMMLREMREGRGPIY
MDTKTALQTSFATMSPAQQKHLEAEAWEDFLDMCVGQANLWAATNCAPEE
RGSEIMPTEPYLLGSHSGCCGIWASGPDEAWVPEDYKVRAANGKVYNRMT
TVEGLWTCADGVGASGHKFSSGSHAEGRIVGKQMVRWYLDHKDFKPEFVE
TAEELKTLIYRPYYNYEKGKGASTCPVVNPEYISPKNFMMRLIKCTDEYG
GGVGTYYNTSKALLDTGFWLMEMLEEDSLKLAARDLHELLRCWENYHRLW
TVRLHMQHIAFREESRYPGFYYRADFLGLDDSKWKCFVNSKYDPAKKETK
IFKKPYYQIIPD

Ligand information

• Ligand ID: FAD
• InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
• InChIKey: VWWQXMAJTJZDQX-UYBVJOGSSA-N
• SMILES:
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
  ACDLabs 10.04: O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
• Formula: C27 H33 N9 O15 P2
• Name: FLAVIN-ADENINE DINUCLEOTIDE
• ChEMBL: CHEMBL1232653
• DrugBank: DB03147
• ZINC: ZINC000008215434
• PDB chain: 3gyx Chain K Residue 1000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3gyx Crystal structure of Adenylylsulfate reductase from Desulfovibrio gigas suggests a potential self-regulation mechanism involving the C terminus of the beta-subunit
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): G32 G33 M34 G35 D60 K61 S67 G68 A69 L74 A76 N78 F192 I193 A230 C231 G232 W251 S259 M385 S417 H418 A461 F471 S472 S475
• Binding residue (residue number reindexed from 1): G30 G31 M32 G33 D58 K59 S65 G66 A67 L72 A74 N76 F190 I191 A228 C229 G230 W249 S257 M383 S415 H416 A459 F469 S470 S473
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): N78 S158 W251 R282 D381 H418 S472
• Catalytic site (residue number reindexed from 1): N76 S156 W249 R280 D379 H416 S470
• Enzyme Commision number: 1.8.99.2: adenylyl-sulfate reductase.

Gene Ontology

Molecular Function

• GO:0000104 succinate dehydrogenase activity
• GO:0000166 nucleotide binding
• GO:0005515 protein binding
• GO:0009055 electron transfer activity
• GO:0009973 adenylyl-sulfate reductase activity
• GO:0016491 oxidoreductase activity
• GO:0046982 protein heterodimerization activity
• GO:0050660 flavin adenine dinucleotide binding
• GO:0071949 FAD binding

Biological Process

• GO:0009061 anaerobic respiration
• GO:0019420 dissimilatory sulfate reduction
• GO:0051290 protein heterotetramerization

Cellular Component

• GO:0005737 cytoplasm
• GO:0005886 plasma membrane

External links

• PDB: RCSB:3gyx, PDBe:3gyx, PDBj:3gyx
• PDBsum: 3gyx
• PubMed: 19820092
• UniProt: T2G6Z9|APRA_MEGG1 Adenylylsulfate reductase subunit alpha (Gene Name=aprA)