Structure of PDB 2vbg Chain A Binding Site BS03

Receptor Information

>2vbg Chain A (length=546) Species: 1358 (Lactococcus lactis)

HSSGLMYTVGDYLLDRLHELGIEEIFGVPGDYNLQFLDQIISREDMKWIG
NANELNASYMADGYARTKKAAAFLTTFGVGELSAINGLAGSYAENLPVVE
IVGSPTSKVQNDGKFVHHTLADGDFKHFMKMHEPVTAARTLLTAENATYE
IDRVLSQLLKERKPVYINLPVDVAAAKAEKPALSLENTTEQVILSKIEES
LKNAQKPVVIAGHEVISFGLEKTVTQFVSETKLPITTLNFGKSAVDESLP
SFLGIYNGKLSEISLKNFVESADFILMLGVKLTDSSTGAFTHHLDENKMI
SLNIDEGIIFNKVVEDFDFRAVVSSLSELKGIEYEGQYIDKQYEEFIPSS
APLSQDRLWQAVESLTQSNETIVAEQGTSFFGASTIFLKSNSRFIGQPLW
GSIGYTFPAALGSQIADKESRHLLFIGDGSLQLTVQELGLSIREKLNPIC
FIINNDGYTVEREIHGPTQSYNDIPMWNYSKLPETFGATEDRVVSKIVRT
ENEFVSVMKEAQADVNRMYWIELVLEKEDAPKLLKKMGKLFAEQNK

Ligand information

• Ligand ID: R1T
• InChI: InChI=1S/C15H23N3O8P2S/c1-8-12(6-11-7-17-10(3)18-15(11)16)14(9(2)19)29-13(8)4-5-25-28(23,24)26-27(20,21)22/h7,9,19H,4-6H2,1-3H3,(H,23,24)(H2,16,17,18)(H2,20,21,22)/t9-/m1/s1
• InChIKey: ORVRYSKZCUVOLA-SECBINFHSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: Cc1c(sc(c1Cc2cnc(nc2N)C)C(C)O)CCOP(=O)(O)OP(=O)(O)O
  OpenEye OEToolkits 1.5.0: Cc1c(sc(c1Cc2cnc(nc2N)C)[C@@H](C)O)CCO[P@](=O)(O)OP(=O)(O)O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCCc1sc(c(c1C)Cc2cnc(nc2N)C)C(O)C
  CACTVS 3.341: C[CH](O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)c1Cc2cnc(C)nc2N
  CACTVS 3.341: C[C@@H](O)c1sc(CCO[P@@](O)(=O)O[P](O)(O)=O)c(C)c1Cc2cnc(C)nc2N
• Formula: C15 H23 N3 O8 P2 S
• Name: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE;
  2-[(1R)-1-HYDROXYETHYL]-3-DEAZA-THDP
• ZINC: ZINC000016052593
• PDB chain: 2vbg Chain B Residue 1549

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2vbg Crystal Structure of the Branched-Chain Keto Acid Decarboxylase (Kdca) from Lactococcus Lactis Provides Insights Into the Structural Basis for the Chemo- and Enantioselective Carboligation Reaction
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): P24 E49 V74 H113
• Binding residue (residue number reindexed from 1): P29 E54 V79 H118
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): V23 G25 D26 Y27 N28 N48 E49 T71 F110 V111 H112 H113 L115 A116 V166 K260 S287 E376 Q377 G402 I404 D429 N456 G458 Y459 V461 E462 K528
• Catalytic site (residue number reindexed from 1): V28 G30 D31 Y32 N33 N53 E54 T76 F115 V116 H117 H118 L120 A121 V171 K259 S286 E375 Q376 G401 I403 D428 N455 G457 Y458 V460 E461 K527

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0004737 pyruvate decarboxylase activity
• GO:0016831 carboxy-lyase activity
• GO:0030976 thiamine pyrophosphate binding
• GO:0046872 metal ion binding
• GO:0047433 branched-chain-2-oxoacid decarboxylase activity

Biological Process

• GO:0000949 aromatic amino acid family catabolic process to alcohol via Ehrlich pathway
• GO:0009082 branched-chain amino acid biosynthetic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:2vbg, PDBe:2vbg, PDBj:2vbg
• PDBsum: 2vbg
• PubMed: 18084069
• UniProt: Q6QBS4