Structure of PDB 1kol Chain A Binding Site BS03

Receptor Information
>1kol Chain A (length=396) Species: 303 (Pseudomonas putida) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GNRGVVYLGSGKVEVQKIDYPKMQDPRGKKIEHGVILKVVSTNICGSDQH
MVRGRTTAQVGLVLGHEITGEVIEKGRDVENLQIGDLVSVPFNVACGRCR
SCKEMHTGVCLTVNPARAGGAYGYVDMGDWTGGQAEYVLVPYADFNLLKL
PDRDKAMEKIRDLTCLSDILPTGYHGAVTAGVGPGSTVYVAGAGPVGLAA
AASARLLGAAVVIVGDLNPARLAHAKAQGFEIADLSLDTPLHEQIAALLG
EPEVDCAVDAVGFEARGHGHEGAKHEAPATVLNSLMQVTRVAGKIGIPGL
YVTEDPGAVDAAAKIGSLSIRFGLGWAKSHSFHTGQTPVMKYNRALMQAI
MWDRINIAEVVGVQVISLDDAPRGYGEFDAGVPKKFVIDPHKTFSA
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain1kol Chain A Residue 1403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1kol Crystal Structure of Formaldehyde Dehydrogenase from Pseudomonas putida: the Structural Origin of the Tightly Bound Cofactor in Nicotinoprotein Dehydrogenases
Resolution1.65 Å
Binding residue
(original residue number in PDB)		C46 G47 S48 H51 F93 D169 T173 G193 G195 P196 V197 D217 L218 R222 A261 V262 R267 H269 V282 P299 L301 Q337 T338
Binding residue
(residue number reindexed from 1)		C45 G46 S47 H50 F92 D168 T172 G192 G194 P195 V196 D216 L217 R221 A260 V261 R266 H268 V281 P298 L300 Q336 T337
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) C46 G47 S48 H51 H67 E68 C97 C100 C103 C111 N115 D169 T173 K386
Catalytic site (residue number reindexed from 1) C45 G46 S47 H50 H66 E67 C96 C99 C102 C110 N114 D168 T172 K385
Enzyme Commision number 1.2.1.46: formaldehyde dehydrogenase.
1.2.98.1: formaldehyde dismutase.
Gene Ontology
Molecular Function
GO:0008270 zinc ion binding
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0018467 formaldehyde dehydrogenase (NAD+) activity
GO:0046872 metal ion binding
GO:0047895 formaldehyde dismutase activity

View graph for
Molecular Function
External links
PDB RCSB:1kol, PDBe:1kol, PDBj:1kol
PDBsum1kol
PubMed12445786
UniProtP46154|FADH_PSEPU Glutathione-independent formaldehyde dehydrogenase (Gene Name=fdhA)

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