Structure of PDB 2c3p Chain B Binding Site BS04

Receptor Information

>2c3p Chain B (length=1231) Species: 873 (Desulfocurvibacter africanus)

GKKMMTTDGNTATAHVAYAMSEVAAIYPITPSSTMGEEADDWAAQGRKNI
FGQTLTIREMQSEAGAAGAVHGALAAGALTTTFTASQGLLLMIPNMYKIS
GELLPGVFHVTARAIAAHALSIFGDHQDIYAARQTGFAMLASSSVQEAHD
MALVAHLAAIESNVPFMHFFDGFRTSHEIQKIEVLDYADMASLVNQKALA
EFRAKSMNPEHPHVRGTAQNPDIYFQGREAANPYYLKVPGIVAEYMQKVA
SLTGRSYKLFDYVGAPDAERVIVSMGSSCETIEEVINHLAAKGEKIGLIK
VRLYRPFVSEAFFAALPASAKVITVLDRTKEPGAPGDPLYLDVCSAFVER
GEAMPKILAGRYGLGSKEFSPAMVKSVYDNMSGAKKNHFTVGIEDDVTGT
SLPVDNAFADTTPKGTIQCQFWGLGADGTVGANKQAIKIIGDNTDLFAQG
YFSYDSKKSGGITISHLRFGEKPIQSTYLVNRADYVACHNPAYVGIYDIL
EGIKDGGTFVLNSPWSSLEDMDKHLPSGIKRTIANKKLKFYNIDAVKIAT
DVGLGGRINMIMQTAFFKLAGVLPFEKAVDLLKKSIHKAYGKKGEKIVKM
NTDAVDQAVTSLQEFKYPDSWKDAPAETKAEPMTNEFFKNVVKPILTQQG
DKLPVSAFEADGRFPLGTSQFEKRGVAINVPQWVPENCIQCNQCAFVCPH
SAILPVLAKEEELVGAPANFTALEAKGKELKGYKFRIQINTLDCMGCGNC
ADICPPKEKALVMQPLDTQRDAQVPNLEYAARIPVKSEVLPRDSLKGSQF
QEPLMEFSGACSGCGETPYVRVITQLFGERMFIANATGCSSIWGASAPSM
PYKTNRLGQGPAWGNSLFEDAAEYGFGMNMSMFARRTHLADLAAKALESD
ASGDVKEALQGWLAGKNDPIKSKEYGDKLKKLLAGQKDGLLGQIAAMSDL
YTKKSVWIFGGDGWAYDIGYGGLDHVLASGEDVNVFVMDTEVYSNTGGQS
SKATPTGAVAKFAAAGKRTGKKDLARMVMTYGYVYVATVSMGYSKQQFLK
VLKEAESFPGPSLVIAYATCINQGLRKGMGKSQDVMNTAVKSGYWPLFRY
DPRLAAQGKNPFQLDSKAPDGSVEEFLMAQNRFAVLDRSFPEDAKRLRAQ
VAHELDVRFKELEHMAATNIFESFAPAGGKADGSVDFGEGAEFCTRDDTP
MMARPDSGEACDQNRAGTSEQQGDLSKRTKK

Ligand information

• Ligand ID: 1TP
• InChI: InChI=1S/C15H26N4O10P2S/c1-8-11(4-5-28-31(26,27)29-30(23,24)25)32-13(15(3,22)14(20)21)19(8)7-10-6-17-9(2)18-12(10)16/h6,8,11,13,22H,4-5,7H2,1-3H3,(H,20,21)(H,26,27)(H2,16,17,18)(H2,23,24,25)/t8-,11-,13+,15+/m0/s1
• InChIKey: TYOXZTVUMWOHPA-JPRMETQZSA-N
• SMILES:
  CACTVS 3.341: C[CH]1[CH](CCO[P](O)(=O)O[P](O)(O)=O)S[CH](N1Cc2cnc(C)nc2N)[C](C)(O)C(O)=O
  OpenEye OEToolkits 1.5.0: Cc1ncc(c(n1)N)CN2C(C(SC2C(C)(C(=O)O)O)CCOP(=O)(O)OP(=O)(O)O)C
  CACTVS 3.341: C[C@H]1[C@H](CCO[P@](O)(=O)O[P](O)(O)=O)S[C@@H](N1Cc2cnc(C)nc2N)[C@@](C)(O)C(O)=O
  OpenEye OEToolkits 1.5.0: Cc1ncc(c(n1)N)C[N@@]2C([C@@H](S[C@@H]2[C@](C)(C(=O)O)O)CCO[P@@](=O)(O)OP(=O)(O)O)C
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCCC2SC(N(Cc1cnc(nc1N)C)C2C)C(O)(C(=O)O)C
• Formula: C15 H26 N4 O10 P2 S
• Name: 1-(2-{(2S,4R,5R)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-[(1S)-1-CARBOXY-1-HYDROXYETHYL]-4-METHYL-1,3-THIAZOLIDIN-5-YL}ETHOXY)-1,1,3,3-TETRAHYDROXY-1LAMBDA~5~-DIPHOSPHOX-1-EN-2-IUM 3-OXIDE
• ZINC: ZINC000058660569
• PDB chain: 2c3p Chain B Residue 2236

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2c3p Flexibility of Thiamine Diphosphate Revealed by Kinetic Crystallographic Studies of the Reaction of Pyruvate-Ferredoxin Oxidoreductase with Pyruvate.
• Resolution: 2.33 Å
• Binding residue (original residue number in PDB): Y28 P29 I30 T31 E64 Q88 R114 E817 T838 C840 F869 G962 D963 G964 V993 Y994 S995 N996 T997
• Binding residue (residue number reindexed from 1): Y27 P28 I29 T30 E63 Q87 R113 E816 T837 C839 F868 G961 D962 G963 V992 Y993 S994 N995 T996
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): T31 E64 R114 N996
• Catalytic site (residue number reindexed from 1): T30 E63 R113 N995
• Enzyme Commision number: 1.2.7.1: pyruvate synthase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0005506 iron ion binding
• GO:0016491 oxidoreductase activity
• GO:0016903 oxidoreductase activity, acting on the aldehyde or oxo group of donors
• GO:0019164 pyruvate synthase activity
• GO:0030976 thiamine pyrophosphate binding
• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0006086 acetyl-CoA biosynthetic process from pyruvate
• GO:0006979 response to oxidative stress
• GO:0022900 electron transport chain

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:2c3p, PDBe:2c3p, PDBj:2c3p
• PDBsum: 2c3p
• PubMed: 16472741
• UniProt: P94692|PFOR_DESAF Pyruvate:ferredoxin oxidoreductase (Gene Name=por)