Structure of PDB 5fem Chain B Binding Site BS03

Receptor Information

>5fem Chain B (length=599) Species: 559292 (Saccharomyces cerevisiae S288C)

PDMDTSFVGLTGGQIFNEMMSRQNVDTVFGYPGGAILPVYDAIHNSDKFN
FVLPKHEQGAGHMAEGYARASGKPGVVLVTSGPGATNVVTPMADAFADGI
PMVVFTGQVPTSAIGTDAFQEADVVGISRSCTKWNVMVKSVEELPLRINE
AFEIATSGRPGPVLVDLPKDVTAAILRNPIPTKTTLPSTSRAQDEFVMQS
INKAADLINLAKKPVLYVGAGILNHADGPRLLKELSDRAQIPVTTTLQGL
GSFDQEDPKSLDMLGMHGCATANLAVQNADLIIAVGARFDDRVTGNISKF
APEARRAAAEGRGGIIHFEVSPKNINKVVQTQIAVEGDATTNLGKMMSKI
FPVKERSEWFAQINKWKKEYPYAYMEETPGSKIKPQTVIKKLSKVANDTG
RHVIVTTGVGQHQMWAAQHWTWRNPHTFITSGGLGTMGYGLPAAIGAQVA
KPESLVIDIDGDASFNMTLTELSSAVQAGTPVKILILNNEEQGMVTQWQS
LFYEHRYSHTHQLNPDFIKLAEAMGLKGLRVKKQEELDAKLKEFVSTKGP
VLLEVEVDKKVPVLPMVAGGSGLDEFINFDPEVERQQTELRHKRTGGKH

Ligand information

• Ligand ID: FAD
• InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
• InChIKey: VWWQXMAJTJZDQX-UYBVJOGSSA-N
• SMILES:
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
  ACDLabs 10.04: O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
• Formula: C27 H33 N9 O15 P2
• Name: FLAVIN-ADENINE DINUCLEOTIDE
• ChEMBL: CHEMBL1232653
• DrugBank: DB03147
• ZINC: ZINC000008215434
• PDB chain: 5fem Chain B Residue 701

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5fem Commercial Herbicides Can Trigger the Oxidative Inactivation of Acetohydroxyacid Synthase.
• Resolution: 2.168 Å
• Binding residue (original residue number in PDB): R241 G307 A308 G309 N312 T334 L335 Q336 L352 G374 A375 R376 R380 V381 E407 V408 N412 G425 D426 A427 M502 G520 G521
• Binding residue (residue number reindexed from 1): R159 G219 A220 G221 N224 T246 L247 Q248 L264 G286 A287 R288 R292 V293 E319 V320 N324 G337 D338 A339 M414 G432 G433
• 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): Y31 G33 G34 A35 I36 E57 T80 F119 Q120 E121 K169 R230 M266 V293 V409 L434 G435 M437 D462 N489 E491 Q492 M494 V495 W498 L520 G525 L526 K559
• 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:5fem, PDBe:5fem, PDBj:5fem
• PDBsum: 5fem
• PubMed: 26924714
• UniProt: P07342|ILVB_YEAST Acetolactate synthase catalytic subunit, mitochondrial (Gene Name=ILV2)