Structure of PDB 2yg4 Chain A Binding Site BS01

Receptor Information

>2yg4 Chain A (length=449) Species: 1833 (Rhodococcus erythropolis)

PTLQRDVAIVGAGPSGLAAATALRKAGLSVAVIEARDRVGGRTWTDTIDG
AVLEIGGQWVSPDQTALISLLDELGLKTFERYREGESVYISSAGERTRYT
GDSFPTNETTKKEMDRLIDEMDDLAAQIGAEEPWAHPLARDLDTVSFKQW
LINQSDDAEARDNIGLFIAGGMLTKPAHSFSALQAVLMAASAGSFSHLVD
EDFILDKRVIGGMQQVSIRMAEALGDDVFLNAPVRTVKWNESGATVLADG
DIRVEASRVILAVPPNLYSRISYDPPLPRRQHQMHQHQSLGLVIKVHAVY
ETPFWREDGLSGTGFGASEVVQEVYDNTNHEDDRGTLVAFVSDEKADAMF
ELSAEERKATILASLARYLGPKAEEPVVYYESDWGSEEWTRGAYAASFDL
GGLHRYGADSRTPVGPIHFSCSDIAAEGYQHVDGAVRMGQRTAADIIAR

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: 2yg4 Chain A Residue 600

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2yg4 Structure-Based Redesign of Cofactor Binding in Putrescine Oxidase.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): V11 G12 G14 P15 S16 E35 A36 R37 G42 R43 G57 G58 Q59 W60 V235 V264 W385 W390 Y395 C422 S423 Q431 H432 V433
• Binding residue (residue number reindexed from 1): V10 G11 G13 P14 S15 E34 A35 R36 G41 R42 G56 G57 Q58 W59 V234 V263 W384 W389 Y394 C421 S422 Q430 H431 V432
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): S62 S197 K296
• Catalytic site (residue number reindexed from 1): S61 S196 K295
• Enzyme Commision number: 1.4.3.10: putrescine oxidase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0016491 oxidoreductase activity

External links

• PDB: RCSB:2yg4, PDBe:2yg4, PDBj:2yg4
• PDBsum: 2yg4
• PubMed: 21486042
• UniProt: B0F9F6