SMTL ID : 3dkl.1

Crystal structure of phosphorylated mimic form of human NAMPT complexed with benzamide and phosphoribosyl pyrophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.313 Ligands: BEF.4, PRP.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.313 MG.2: 2 residues within 4Å: Chain A: R.40 Ligands: PRP.8 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: R.40 Ligands: PRP.7 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain B: R.311, D.313 Ligands: PRP.8, BEF.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.313

2 x UNU: BENZAMIDE(Non-covalent)

UNU.3: 8 residues within 4Å: Chain A: F.193, R.196, D.219, A.244, R.311 Chain B: D.16, Y.18 Ligands: PRP.7 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A pi-Stacking: B:Y.18, A:F.193 Hydrophobic interactions: A:F.193, A:D.219 Hydrogen bonds: A:D.219 UNU.9: 8 residues within 4Å: Chain A: D.16, Y.18 Chain B: F.193, R.196, D.219, A.244, R.311 Ligands: PRP.8 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:D.16, B:F.193, B:D.219 pi-Stacking: A:Y.18, B:F.193 Hydrogen bonds: B:D.219

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)

BEF.4: 7 residues within 4Å: Chain A: E.246, H.247, D.313 Chain B: K.400, K.415 Ligands: MG.1, PRP.7 No protein-ligand interaction detected (PLIP) BEF.10: 7 residues within 4Å: Chain A: K.400, K.415 Chain B: E.246, H.247, D.313 Ligands: MG.6, PRP.8 No protein-ligand interaction detected (PLIP)

2 x PRP: 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose(Non-covalent)

PRP.7: 15 residues within 4Å: Chain A: R.196, R.311, D.313, G.353, G.383, G.384 Chain B: R.40, R.392, K.400, K.415, K.423 Ligands: MG.1, UNU.3, BEF.4, MG.5 31 PLIP interactions: 12 interactions with chain A, 19 interactions with chain B Hydrogen bonds: A:R.311, A:R.311, A:D.313, A:G.383, A:G.384, B:K.423 Water bridges: A:R.196, A:D.354, A:D.354, A:G.355, A:G.385, B:R.40, B:R.392, B:R.392, B:R.392, B:R.392, B:R.392, B:R.392, B:R.392, B:D.393, B:K.415 Salt bridges: A:R.196, A:R.196, B:R.40, B:R.392, B:R.392, B:R.392, B:K.400, B:K.400, B:K.415, B:K.423 PRP.8: 15 residues within 4Å: Chain A: R.40, R.392, K.400, K.415, K.423 Chain B: R.196, R.311, D.313, G.353, G.383, G.384 Ligands: MG.2, MG.6, UNU.9, BEF.10 32 PLIP interactions: 14 interactions with chain B, 18 interactions with chain A Hydrogen bonds: B:R.311, B:R.311, B:D.313, B:G.383, B:G.384, A:K.423 Water bridges: B:R.196, B:R.196, B:R.196, B:G.353, B:G.355, B:V.356, B:G.385, A:R.40, A:R.392, A:R.392, A:R.392, A:R.392, A:R.392, A:D.393, A:K.415 Salt bridges: B:R.196, B:R.196, A:R.40, A:R.392, A:R.392, A:R.392, A:K.400, A:K.400, A:K.400, A:K.415, A:K.423

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burgos, E.S. et al., A phosphoenzyme mimic, overlapping catalytic sites and reaction coordinate motion for human NAMPT. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-08-18

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

Related Entries With Identical Sequence