Structure of PDB 6cip Chain F Binding Site BS04

Receptor Information

>6cip Chain F (length=1169) Species: 264732 (Moorella thermoacetica ATCC 39073)

PKQTLDGNTAAAHVAYAMSEVATIYPITPSSPMAEIADEWAAHGRKNIFG
KTLQVAEMQSEAGAAGAVHGSLAAGALTTTFTASQGLLLMIPNMYKIAGE
LLPCVFHVAARALSTHALSIFGDHADVMAARQTGFAMLSSASVQEVMDLA
LVAHLATLKARVPFVHFFDGFRTSHEVQKIDVIEYEDMAKLVDWDAIRAF
RQRALNPEHPHQRGTAQNPDIYFQSREAANPYYLATPGIVAQVMEQVAGL
TGRHYHLFDYAGAPDAERVIVSMGSSCEVIEETVNYLVEKGEKVGLIKVR
LFRPFSAEHFLKVLPASVKRIAVLDRTKEPGSLGEPLYEDVQTVLAEHGK
NILVVGGRYGLGSKEFNPSMVKAVFDNLAATTPKNKFTVGITDDVTHTSL
EIKEHIDTSPKGTFRCKFFGLGSDGTVGANKNSIKIIGDHTDMYAQGYFV
YDSKKSGGVTISHLRFGKQPIQSAYLIDQADLIACHNPSYVGRYNLLEGI
KPGGIFLLNSTWSAEEMDSRLPADMKRTIATKKLKFYNIDAVKIAQEIGL
GSRINVIMQTAFFKIANVIPVDEAIKYIKDSIVKTYGKKGDKILNMNFAA
VDRALEALEEIKYPASWADAVDEAAATVTEEPEFIQKVLRPINALKGDEL
PVSTFTPDGVFPVGTTKYEKRGIAVNIPQWQPENCIQCNQCSLVCPHAAI
RPYLAKPADLAGAPETFVTKDAIGKEAAGLKFRIQVSPLDCTGCGNCADV
CPAKVKALTMVPLEEVTAVEEANYNFAEQLPEVKVNFNPATVKGSQFRQP
LLEFSGACAGCGETPYVKLVTQLFGDRMIIANATGCSSIWGGSAPACPYT
VNRQGHGPAWASSLFEDNAEFGYGMALAVAKRQDELATAISKALEAPVSA
AFKAACEGWLAGKDDADRSREYGDRIKALLPGEISQASGEVKDLLLDIDR
QKDYLTKKSIWIIGGDGWAYDIGYGGLDHVLASGANVNVLVLDTEVYSNT
GGQSSKATQTGAVARFAAGGKFTKKKDLGLMAMSYGYVYVASVAMGASHS
QLMKALIEAEKYDGPSLIIAYAPCINHGINMTYSQREAKKAVEAGYWPLY
RYNPQLAQEGKNPFILDYKTPTASFRDFLMGEIRYTSLKKQFPEKAEQLF
AKAEADAKARLEQYKKLAE

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: 6cip Chain F Residue 1204

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6cip Binding site for coenzyme A revealed in the structure of pyruvate:ferredoxin oxidoreductase fromMoorella thermoacetica.
• Resolution: 3.189 Å
• Binding residue (original residue number in PDB): P27 I28 E62 R112 E814 T835 G836 C837 F866 G966 D967 G968 V997 Y998 S999 N1000 T1001
• Binding residue (residue number reindexed from 1): P26 I27 E61 R111 E813 T834 G835 C836 F865 G965 D966 G967 V996 Y997 S998 N999 T1000
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): T29 E62 R112 N1000
• Catalytic site (residue number reindexed from 1): T28 E61 R111 N999
• 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

External links

• PDB: RCSB:6cip, PDBe:6cip, PDBj:6cip
• PDBsum: 6cip
• PubMed: 29581263
• UniProt: Q2RMD6|PFOR_MOOTA Pyruvate:ferredoxin oxidoreductase (Gene Name=Moth_0064)