Structure of PDB 1xd9 Chain A Binding Site BS03

Receptor Information
>1xd9 Chain A (length=289) Species: 354 (Azotobacter vinelandii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AMRQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCNPKADSTRLILH
SKAQNTIMEMAAEAGTVEDLELEDVLKAGYGGVKCVESGGPEPGVGCAGR
GVITAINFLEEEGAYEDDLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIV
CSGEMMAMYAANNISKGIVKYANSGSVRLGGLICNSRNTDREDELIIALA
NKLGTQMIHFVPRDNVVQRAEIRRMTVIEYDPKAKQADEYRALARKVVDN
KLLVIPNPITMDELEELLMEFGIMEVEDESIVGKTAEEV
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain1xd9 Chain A Residue 291 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1xd9 Structural and biochemical implications of single amino acid substitutions in the nucleotide-dependent switch regions of the nitrogenase Fe protein from Azotobacter vinelandii
Resolution2.8 Å
Binding residue
(original residue number in PDB)		G12 G14 K15 S16 T17 R213 D214 V217 E221
Binding residue
(residue number reindexed from 1)		G12 G14 K15 S16 T17 R213 D214 V217 E221
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K10 K15 K41 D129
Catalytic site (residue number reindexed from 1) K10 K15 K41 D129
Enzyme Commision number 1.18.6.1: nitrogenase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016163 nitrogenase activity
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0009399 nitrogen fixation

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Molecular Function
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Biological Process
External links
PDB RCSB:1xd9, PDBe:1xd9, PDBj:1xd9
PDBsum1xd9
PubMed15549494
UniProtP00459|NIFH1_AZOVI Nitrogenase iron protein 1 (Gene Name=nifH1)

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