Structure of PDB 3ntd Chain B Binding Site BS02

Receptor Information

>3ntd Chain B (length=565) Species: 323850 (Shewanella loihica PV-4)

MKKILIIGGVAGGASAAARARRLSETAEIIMFERGEYVSFANCGLPYHIS
GEIAQRSALVLQTPESFKARFNVEVRVKHEVVAIDRAAKLVTVRRLLDGS
EYQESYDTLLLSPGAAPIVPPIPGVDNPLTHSLRNIPDMDRILQTIQMNN
VEHATVVGGGFIGLEMMESLHHLGIKTTLLELADQVMTPVDREMAGFAHQ
AIRDQGVDLRLGTALSEVSYQVQTHVASDAAGEDTAHQHIKGHLSLTLSN
GELLETDLLIMAIGVRPETQLARDAGLAIGELGGIKVNAMMQTSDPAIYA
VGDAVEEQDFVTGQACLVPLAGPANRQGRMAADNMFGREERYQGTQGTAI
CKVFDLAVGATGKNEKQLKQAGIAFEKVYVHTASHASYYPGAEVVSFKLL
FDPVKGTIFGAQAVGKDGIDKRIDVMAVAQRAGMTVEQLQHLELSYAPPY
GSAKDVINQAAFVASNIIKGDATPIHFDQIDNLSEDQLLLDVRNPGELQN
GGLEGAVNIPVDELRDRMHELPKDKEIIIFSQVGLRGNVAYRQLVNNGYR
ARNLIGGYRTYKFAS

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: 3ntd Chain B Residue 900

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3ntd Characterization of an NADH-Dependent Persulfide Reductase from Shewanella loihica PV-4: Implications for the Mechanism of Sulfur Respiration via FAD-Dependent Enzymes .
• Resolution: 1.99 Å
• Binding residue (original residue number in PDB): G8 V10 A11 G12 E33 R34 N42 C43 E80 V81 S112 P113 G114 L133 F161 I162 G302 D303 P319 L320 A321
• Binding residue (residue number reindexed from 1): G8 V10 A11 G12 E33 R34 N42 C43 E80 V81 S112 P113 G114 L133 F161 I162 G302 D303 P319 L320 A321
• Annotation score: 2

Enzymatic activity

• Catalytic site (original residue number in PDB): A11 V38 N42 C43 N325 D471 A472
• Catalytic site (residue number reindexed from 1): A11 V38 N42 C43 N325 D471 A472
• Enzyme Commision number: 1.8.1.14: CoA-disulfide reductase.

Gene Ontology

Molecular Function

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

External links

• PDB: RCSB:3ntd, PDBe:3ntd, PDBj:3ntd
• PDBsum: 3ntd
• PubMed: 21090815
• UniProt: A3QAV3