SMTL ID : 3dkj.1

Crystal structure of human NAMPT complexed with benzamide and phosphoribosyl pyrophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

PRP.1: 14 residues within 4Å: Chain A: R.196, R.311, D.313, G.353, D.354, G.383, G.384, G.385 Chain B: R.40, R.392, S.398, K.400, K.423 Ligands: UNU.2 33 PLIP interactions: 16 interactions with chain A, 17 interactions with chain B Hydrogen bonds: A:R.311, A:D.313, A:D.313, A:D.354, A:G.383, A:G.384, A:G.385, B:S.398, B:K.423 Water bridges: A:R.196, A:R.196, A:R.311, A:G.353, A:G.355, A:V.356, A:V.356, B:R.40, B:E.149, B:R.392, B:R.392, B:F.399, B:K.415 Salt bridges: A:R.196, A:R.196, B:R.40, B:R.392, B:R.392, B:R.392, B:R.392, B:K.400, B:K.400, B:K.415, B:K.423 PRP.3: 13 residues within 4Å: Chain A: R.40, R.392, S.398, K.400, K.423 Chain B: R.196, R.311, D.313, G.353, D.354, G.383, G.384 Ligands: UNU.4 31 PLIP interactions: 12 interactions with chain B, 19 interactions with chain A Hydrogen bonds: B:R.311, B:R.311, B:D.313, B:D.313, B:G.383, B:G.384 Water bridges: B:R.196, B:R.196, B:G.355, B:G.355, A:R.40, A:R.392, A:R.392, A:R.392, A:R.392, A:R.392, A:F.399, A:K.415, A:K.415, A:K.423 Salt bridges: B:R.196, B:R.196, A:R.40, A:R.392, A:R.392, A:R.392, A:R.392, A:K.400, A:K.400, A:K.415, A:K.423

2 x UNU: BENZAMIDE(Non-covalent)

UNU.2: 8 residues within 4Å: Chain A: F.193, R.196, D.219, A.244, R.311 Chain B: D.16, Y.18 Ligands: PRP.1 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.193 Hydrogen bonds: A:D.219 Water bridges: A:A.245 pi-Stacking: A:F.193, B:Y.18 UNU.4: 8 residues within 4Å: Chain A: D.16, Y.18 Chain B: F.193, R.196, D.219, A.244, R.311 Ligands: PRP.3 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.193, B:D.219 Hydrogen bonds: B:D.219 pi-Stacking: B:F.193, A:Y.18

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

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