Structure of PDB 3haz Chain A Binding Site BS02

Receptor Information

>3haz Chain A (length=983) Species: 224911 (Bradyrhizobium diazoefficiens USDA 110)

MPNIPPPFTAPYAPDDAEIAARLLPASHLSPPQEARIHRTATRLIEAIRK
RRLGGVEDMLREFALSTKEGLALMVLAEALLRVPDARTADQFIEDKLGEG
DFIHHETKSTAFLVNASAWAARVIQPGETPDGTIGRLVKRLGAPAVRTAT
RQAMRLMGNHFVLGETIEQALERGKPRSGQKTRYSFDMLGEGARTAADAR
RYFDAYASAIETIGKAAGNHALPDRPGISVKLSALHPRFEAISRARVMVE
LVPQLLDLAQRAKAHDLNFTVDAEEADRLELSLDVIAATLADPSLKGWDG
FGLAIQAYQKRASAVIDYVDALARAHDRKLMVRLVKGAYWDTEIKRAQER
GLDGYPVFTRKAMTDLNYVACASKLLALRPRIFPQFATHNALTVATVLEM
AEGSSGFEFQRLHGMGEALYEQLAKDHADIAYRTYAPVGSHRDLLAYLVR
RLLENGANSSFVAQAADYRVPVPALLQRPADAIVRPQAAAHPRIPLPCDL
FAPERRNSRGVEFGARTALDQLLTDVKAETGDLKPIADATPDQAHAAVAA
ARAGFAGWSRTPAGIRAAALEQAAHLLESRSAHFIALLQREGGKTLDDAL
SELREAADFCRYYAAQGRKLFGSETAMPGPTGESNALTMRGRGVFVAISP
WNFPLAIFLGQVTAALMAGNSVVAKPAEQTPRIAREAVALLHEAGIPKSA
LYLVTGDGRIGAALTAHPDIAGVVFTGSTEVARSINRALAAKDGPIVPLI
AETGGINAMIADATALPEQVADDVVTSAFRSAGQRCSALRLLFVQEDVAD
RMIEMVAGAARELKIGDPSDVATHVGPVIDVEAKQRLDAHIARMKTEARL
HFAGPAPEGCFVAPHIFELTEAGQLTEEVFGPILHVVRYRPENLERVLRA
IERTGYGLTLGVHSRIDDSIEAIIDRVQVGNIYVNRNMIGAVVGVQPFGG
NGLSGTGPKAGGPHYLARFATEQTVTINTAAAG

Ligand information

• Ligand ID: NAD
• InChI: InChI=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
• InChIKey: BAWFJGJZGIEFAR-NNYOXOHSSA-N
• SMILES:
  CACTVS 3.341: NC(=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 1.5.0: c1cc(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 3.341: NC(=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 1.5.0: c1cc(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
• Formula: C21 H27 N7 O14 P2
• Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
• ChEMBL: CHEMBL1234613
• DrugBank: DB14128
• PDB chain: 3haz Chain A Residue 2003

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3haz Crystal structure of the bifunctional proline utilization A flavoenzyme from Bradyrhizobium japonicum
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): I654 S655 P656 W657 N658 I663 K681 P682 A683 G714 G717 A718 T732 G733 S734 V737 I741 E758 T759 C792 E884 F886 F954
• Binding residue (residue number reindexed from 1): I648 S649 P650 W651 N652 I657 K675 P676 A677 G708 G711 A712 T726 G727 S728 V731 I735 E752 T753 C786 E878 F880 F948
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): N658 K681 E758 C792 E884 A966
• Catalytic site (residue number reindexed from 1): N652 K675 E752 C786 E878 A960
• Enzyme Commision number: 1.2.1.88: L-glutamate gamma-semialdehyde dehydrogenase.
  1.5.5.2: proline dehydrogenase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003677 DNA binding
• GO:0003700 DNA-binding transcription factor activity
• GO:0003842 1-pyrroline-5-carboxylate dehydrogenase activity
• GO:0004657 proline dehydrogenase activity
• GO:0016491 oxidoreductase activity
• GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
• GO:0042802 identical protein binding

Biological Process

• GO:0006355 regulation of DNA-templated transcription
• GO:0006560 proline metabolic process
• GO:0006561 proline biosynthetic process
• GO:0006562 proline catabolic process
• GO:0010133 proline catabolic process to glutamate

Cellular Component

• GO:0009898 cytoplasmic side of plasma membrane

External links

• PDB: RCSB:3haz, PDBe:3haz, PDBj:3haz
• PDBsum: 3haz
• PubMed: 20133651
• UniProt: Q89E26