Structure of PDB 2gq3 Chain A Binding Site BS03

Receptor Information

>2gq3 Chain A (length=720) Species: 1773 (Mycobacterium tuberculosis)

TDRVSVGNLRIARVLYDFVNNEALPGTDIDPDSFWAGVDKVVADLTPQNQ
ALLNARDELQAQIDKWHRRRPIDMDAYRQFLTEIGYLLPEPDDFTITTSG
VDAEITTTAGPQLVVPVLNARFALNAANARWGSLYDALYGTDVIPETDGA
EKGPTYNKVRGDKVIAYARKFLDDSVPLSSGSFGDATGFTVQDGQLVVAL
PDKSTGLANPGQFAGYTGAAESPTSVLLINHGLHIEILIDPESQVGTTDR
AGVKDVILESAITTIMDFEDSVAAVDAADKVLGYRNWLGLNKGDLAAAVD
KDGTAFLRVLNRDRNYTAPGGGQFTLPGRSLMFVRNVGHLMTNDAIVDTD
GSEVFEGIMDALFTGLIAIHGLKASDVNGPLINSRTGSIYIVKPKMHGPA
EVAFTCELFSRVEDVLGLPQNTMKIGIMDEERRTTVNLKACIKAAADRVV
FINTGFLDRTGDEIHTSMEAGPMVRKGTMKSQPWILAYEDHNVDAGLAAG
FSGRAQVGKGMWTMTELMADMVETKIAQPRAGASTAWVPSPTAATLHALH
YHQVDVAAVQQGLAGKRRATIEQLLTIPLAKWAPDEIREEVDNNCQSILG
YVVRWVDQGVGCSKVPDIHDVALMEDRATLRISSQLLANWLRHGVITSAD
VRASLERMAPLVDRQNAGDVAYRPMAPNFDDSIAFLAAQELILSGAQQPN
GYTEPILHRRRREFKARAAE

Ligand information

• Ligand ID: COA
• InChI: InChI=1S/C21H36N7O16P3S/c1-21(2,16(31)19(32)24-4-3-12(29)23-5-6-48)8-41-47(38,39)44-46(36,37)40-7-11-15(43-45(33,34)35)14(30)20(42-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-31,48H,3-8H2,1-2H3,(H,23,29)(H,24,32)(H,36,37)(H,38,39)(H2,22,25,26)(H2,33,34,35)/t11-,14-,15-,16+,20-/m1/s1
• InChIKey: RGJOEKWQDUBAIZ-IBOSZNHHSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCS)O
  CACTVS 3.341: CC(C)(CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCS
  OpenEye OEToolkits 1.5.0: CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS)O
  CACTVS 3.341: CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCS
  ACDLabs 10.04: O=C(NCCS)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
• Formula: C21 H36 N7 O16 P3 S
• Name: COENZYME A
• ChEMBL: CHEMBL1213327
• DrugBank: DB01992
• ZINC: ZINC000008551087
• PDB chain: 2gq3 Chain A Residue 800

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2gq3 The product complex of M. tuberculosis malate synthase revisited.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): V118 V119 R125 F126 N129 A130 K305 R312 P543 P545 C619 M631 D633
• Binding residue (residue number reindexed from 1): V114 V115 R121 F122 N125 A126 K301 R308 P539 P541 C612 M624 D626
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): D271 E273 R339 E434 D462 D633
• Catalytic site (residue number reindexed from 1): D267 E269 R335 E430 D458 D626
• Enzyme Commision number: 2.3.3.9: malate synthase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0001968 fibronectin binding
• GO:0003824 catalytic activity
• GO:0004474 malate synthase activity
• GO:0005515 protein binding
• GO:0005518 collagen binding
• GO:0016740 transferase activity
• GO:0042803 protein homodimerization activity
• GO:0043236 laminin binding
• GO:0046810 host cell extracellular matrix binding
• GO:0046872 metal ion binding
• GO:0120225 coenzyme A binding

Biological Process

• GO:0006097 glyoxylate cycle
• GO:0006099 tricarboxylic acid cycle
• GO:0009436 glyoxylate catabolic process
• GO:0015936 coenzyme A metabolic process
• GO:0044406 adhesion of symbiont to host

Cellular Component

• GO:0005576 extracellular region
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005886 plasma membrane
• GO:0009274 peptidoglycan-based cell wall
• GO:0009986 cell surface
• GO:0042603 capsule

External links

• PDB: RCSB:2gq3, PDBe:2gq3, PDBj:2gq3
• PDBsum: 2gq3
• PubMed: 16877713
• UniProt: P9WK17|MASZ_MYCTU Malate synthase G (Gene Name=glcB)