Structure of PDB 6bd3 Chain B Binding Site BS03

Receptor Information

>6bd3 Chain B (length=558) Species: 4932 (Saccharomyces cerevisiae)

DMDTSFVGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFNF
VLPKHEQGAGHMAEGYARASGKPGVVLVTSGPGATNVVTPMADAFADGIP
MVVFTGQVPTSAIGTDAFQEADVVGISRSCTKWNVMVKSVEELPLRINEA
FEIATSGRPGPVLVDLPKDVTAAILRNPIPTKTTLPSQLTSRAQDEFVMQ
SINKAADLINLAKKPVLYVGAGILNHADGPRLLKELSDRAQIPVTTTLQG
LGSFDQEDPKSLDMLGMHGCATANLAVQNADLIIAVGARFDDRVTGNISK
FAPEARRAAAEGRGGIIHFEVSPKNINKVVQTQIAVEGDATTNLGKMMSK
IFPVKERSEWFAQINKWKKEYPYAYMEETPGSKIKPQTVIKKLSKVANDT
GRHVIVTTGVGQHQMWAAQHWTWRNPHTFITSGGLGTMGYGLPAAIGAQV
AKPESLVIDIDGDASFNMTLTELSSAVQAGTPVKILILNNEEQGMVTQWQ
SLFYSHTHQLNPDFIKLAEAMGLKGLRVKKQEELDAKLKEFVSTKGPVLL
EVEVDKKV

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: 6bd3 Chain B Residue 703

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6bd3 High resolution crystal structures of the acetohydroxyacid synthase-pyruvate complex provide new insights into its catalytic mechanism
• Resolution: 2.28 Å
• Binding residue (original residue number in PDB): Q499 H500 G523 M525 G549 D550 A551 S552 M555 N577
• Binding residue (residue number reindexed from 1): Q412 H413 G436 M438 G462 D463 A464 S465 M468 N490
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Y113 G115 G116 A117 I118 E139 T162 F201 Q202 E203 K251 R318 M354 V381 V497 L522 G523 M525 D550 N577 E579 Q580 M582 V583 W586 L608 G613 L614 K647
• Catalytic site (residue number reindexed from 1): Y30 G32 G33 A34 I35 E56 T79 F118 Q119 E120 K168 R231 M267 V294 V410 L435 G436 M438 D463 N490 E492 Q493 M495 V496 W499 L517 G522 L523 K556
• Enzyme Commision number: 2.2.1.6: acetolactate synthase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0003984 acetolactate synthase activity
• GO:0016740 transferase activity
• GO:0030976 thiamine pyrophosphate binding
• GO:0046872 metal ion binding
• GO:0050660 flavin adenine dinucleotide binding

Biological Process

• GO:0008652 amino acid biosynthetic process
• GO:0009082 branched-chain amino acid biosynthetic process
• GO:0009097 isoleucine biosynthetic process
• GO:0009099 L-valine biosynthetic process

Cellular Component

• GO:0005739 mitochondrion
• GO:0005948 acetolactate synthase complex

External links

• PDB: RCSB:6bd3, PDBe:6bd3, PDBj:6bd3
• PDBsum: 6bd3
• UniProt: P07342|ILVB_YEAST Acetolactate synthase catalytic subunit, mitochondrial (Gene Name=ILV2)