Structure of PDB 2c3y Chain B Binding Site BS04

Receptor Information

>2c3y Chain B (length=1230) 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
MMARPDSGEACDQNRAGTSEQQGDLSKRTK

Ligand information

• Ligand ID: HTL
• InChI: InChI=1S/C14H20N4O8P2S/c1-8-12(4-5-25-28(23,24)26-27(20,21)22)29-14(9(2)19)18(8)7-11-6-16-10(3)17-13(11)15/h6H,4-5,7H2,1-3H3,(H4-,15,16,17,20,21,22,23,24)/p+1
• InChIKey: GYRGKLZCJRVYRV-UHFFFAOYSA-O
• SMILES:
  ACDLabs 10.04: O=C(c1sc(c([n+]1Cc2cnc(nc2N)C)C)CCOP(=O)(O)OP(=O)(O)O)C
  OpenEye OEToolkits 1.5.0: Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(=O)C)CCO[P@@](=O)(O)OP(=O)(O)O
  CACTVS 3.341: CC(=O)c1sc(CCO[P@](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N
  CACTVS 3.341: CC(=O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N
  OpenEye OEToolkits 1.5.0: Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(=O)C)CCOP(=O)(O)OP(=O)(O)O
• Formula: C14 H21 N4 O8 P2 S
• Name: 2-ACETYL-THIAMINE DIPHOSPHATE;
  2-ACETYL-3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-4-METHYL-5-(4,6,6-TRIHYDROXY-3,5-DIOXA-4,6-DIPHOSPHAHEX-1-YL)THIAZO LIUM INNER SALT P,P'-DIOXIDE
• DrugBank: DB02410
• ZINC: ZINC000013546639
• PDB chain: 2c3y Chain B Residue 2236

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2c3y Flexibility of Thiamine Diphosphate Revealed by Kinetic Crystallographic Studies of the Reaction of Pyruvate-Ferredoxin Oxidoreductase with Pyruvate.
• Resolution: 1.93 Å
• Binding residue (original residue number in PDB): Y28 P29 I30 E64 R114 E817 T838 G839 C840 F869 G962 D963 G964 V993 Y994 S995 N996 T997
• Binding residue (residue number reindexed from 1): Y27 P28 I29 E63 R113 E816 T837 G838 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:2c3y, PDBe:2c3y, PDBj:2c3y
• PDBsum: 2c3y
• PubMed: 16472741
• UniProt: P94692|PFOR_DESAF Pyruvate:ferredoxin oxidoreductase (Gene Name=por)