Structure of PDB 6n2o Chain D Binding Site BS03

Receptor Information

>6n2o Chain D (length=291) Species: 156889 (Magnetococcus marinus MC-1)

TVEAFHKMENMKPKDYKSEVPTTWCPGCGHFGILNGVYRAMAELGIDSTK
FAAISGIGCSSRMPYFVDSYKMHTLHGRAGAVATGTQVARPDLCVVVAGG
DGDGFSIGGGHMPHMARKNVNMTYVLMDNGIYGLTKGQYSPTSRPEMTAY
TTPYGGPENPMNPLLYMLTYGATYVAQAFAGKPKDCAELIKGAMEHEGFA
YVNIFSQCPTFNKIDTVDFYRDLVEPIPEDHDTSDLGAAMELARRPGGKA
PTGLLYKTSAPTLDQNLAKIRERLGGHVGYDKNKIIALAKP

Ligand information

• Ligand ID: TPP
• InChI: InChI=1S/C12H18N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21)/p+1
• InChIKey: AYEKOFBPNLCAJY-UHFFFAOYSA-O
• SMILES:
  CACTVS 3.341: Cc1ncc(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
  OpenEye OEToolkits 1.5.0: Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
  OpenEye OEToolkits 1.5.0: Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O
  CACTVS 3.341: Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N
• Formula: C12 H19 N4 O7 P2 S
• Name: THIAMINE DIPHOSPHATE
• ChEMBL: CHEMBL1236376
• ZINC: ZINC000008215517
• PDB chain: 6n2o Chain D Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6n2o A reverse TCA cycle 2-oxoacid:ferredoxin oxidoreductase that makes C-C bonds from CO2.
• Resolution: 2.824 Å
• Binding residue (original residue number in PDB): I58 G59 C60 S61 H77 G103 D104 N130 I132 G134 L135 T136
• Binding residue (residue number reindexed from 1): I57 G58 C59 S60 H76 G102 D103 N129 I131 G133 L134 T135
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0016491 oxidoreductase activity
• GO:0030976 thiamine pyrophosphate binding
• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding

External links

• PDB: RCSB:6n2o, PDBe:6n2o, PDBj:6n2o
• PDBsum: 6n2o
• PubMed: 31080943
• UniProt: A0L8G5