Structure of PDB 5eso Chain C Binding Site BS01

Receptor Information

>5eso Chain C (length=543) Species: 83332 (Mycobacterium tuberculosis H37Rv)

NPSTTQARVVVDELIRGGVRDVVLCPGSRNAPLAFALQDADRSGRIRLHV
RIDERTAGYLAIGLAIGAGAPVCVAMTSGTAVANLGPAVVEANYARVPLI
VLSANRPYELLGTGANQTMEQLGYFGTQVRASISLGLAEDAPERTSALNA
TWRSATCRVLAAATGARTANAGPVHFDIPLREPVTPPGRPAGKPWTYTPP
VTFDQPLDIDLSVDTVVISGHGAGVHPNLAALPTVAEPTAPRSGDNPLHP
LALPLLRPQQVIMLGRPTLHRPVSVLLADAEVPVFALTTGPRWPDVSGNS
QATGTRAVTTGAPRPAWLDRCAAMNRHAIAAVREQLAAHPLTTGLHVAAA
VSHALRPGDQLVLGASNPVRDVALAGLDTRGIRVRSNRGVAGIDGTVSTA
IGAALAYEGAHERTGSPDSPPRTIALIGDLTFVHDSSGLLIGPTEPIPRS
LTIVVSNDNGGGIFELLEQGDPRFSDVSSRIFGTPHDVDVGALCRAYHVE
SRQIEVDELGPTLDQPGAGMRVLEVKADRSSLRQLHAAIKAAL

Ligand information

• Ligand ID: ISC
• InChI: InChI=1S/C10H10O6/c1-5(9(12)13)16-7-4-2-3-6(8(7)11)10(14)15/h2-4,7-8,11H,1H2,(H,12,13)(H,14,15)/t7-,8-/m0/s1
• InChIKey: NTGWPRCCOQCMGE-YUMQZZPRSA-N
• SMILES:
  ACDLabs 12.01: O=C(O)C1=CC=CC(O/C(C(=O)O)=C)C1O
  OpenEye OEToolkits 1.7.2: C=C(C(=O)O)O[C@H]1C=CC=C([C@@H]1O)C(=O)O
  CACTVS 3.370: O[C@@H]1[C@@H](OC(=C)C(O)=O)C=CC=C1C(O)=O
  CACTVS 3.370: O[CH]1[CH](OC(=C)C(O)=O)C=CC=C1C(O)=O
  OpenEye OEToolkits 1.7.2: C=C(C(=O)O)OC1C=CC=C(C1O)C(=O)O
• Formula: C10 H10 O6
• Name: (5S,6S)-5-[(1-carboxyethenyl)oxy]-6-hydroxycyclohexa-1,3-diene-1-carboxylic acid;
  ISOCHORISMIC ACID
• PDB chain: 5eso Chain B Residue 602

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5eso Structural Views along the Mycobacterium tuberculosis MenD Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms.
• Resolution: 2.05 Å
• Binding residue (original residue number in PDB): R282 L478
• Binding residue (residue number reindexed from 1): R271 L467
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): C26 E55
• Catalytic site (residue number reindexed from 1): C25 E54
• Enzyme Commision number: 2.2.1.9: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0016740 transferase activity
• GO:0030145 manganese ion binding
• GO:0030976 thiamine pyrophosphate binding
• GO:0046872 metal ion binding
• GO:0070204 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity

Biological Process

• GO:0009234 menaquinone biosynthetic process

Cellular Component

• GO:0005886 plasma membrane

External links

• PDB: RCSB:5eso, PDBe:5eso, PDBj:5eso
• PDBsum: 5eso
• PubMed: 27291649
• UniProt: P9WK11|MEND_MYCTU 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (Gene Name=menD)