SMTL ID : 3dhd.1

Crystal structure of human NAMPT complexed with nicotinamide mononucleotide and pyrophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.313 Ligands: NMN.3, POP.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.313, H2O.1 MG.2: 2 residues within 4Å: Chain A: R.392 Ligands: POP.4 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain B: R.40, R.392, K.423 Ligands: POP.7 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: D.313 Ligands: POP.4, NMN.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.313, H2O.8

2 x NMN: BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE(Non-covalent)

NMN.3: 16 residues within 4Å: Chain A: F.193, R.196, D.219, A.244, R.311, D.313, G.353, S.382, G.383, G.384 Chain B: D.16, Y.18, R.392, D.393 Ligands: MG.1, POP.7 22 PLIP interactions: 13 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:F.193, B:Y.18, B:Y.18 Hydrogen bonds: A:D.219, A:R.311, A:R.311, A:D.313, A:G.383, A:G.384, B:D.393 Water bridges: A:D.354, A:D.354, A:G.355, A:V.356, A:G.385, B:R.392, B:R.392, B:R.392, B:R.392, B:K.423 pi-Stacking: A:F.193 Salt bridges: B:R.392 NMN.8: 15 residues within 4Å: Chain A: D.16, Y.18, R.392 Chain B: F.193, R.196, D.219, A.244, R.311, D.313, G.353, S.382, G.383, G.384 Ligands: POP.4, MG.6 22 PLIP interactions: 11 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:F.193, A:Y.18, A:Y.18 Hydrogen bonds: B:D.219, B:R.311, B:R.311, B:D.313, B:G.383, B:G.384 Water bridges: B:G.355, B:G.385, B:G.385, A:R.392, A:R.392, A:R.392, A:R.392, A:D.393, A:D.393, A:K.423, A:K.423 pi-Stacking: B:F.193 Salt bridges: A:R.392

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.4: 11 residues within 4Å: Chain A: R.40, R.392, S.398, K.400, K.415, K.423 Chain B: R.196, D.313 Ligands: MG.2, MG.6, NMN.8 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain B Water bridges: A:R.40, A:R.392, A:R.392, A:K.400, A:K.415, A:K.423, A:K.423, A:K.423, B:R.196, B:R.196, B:D.313 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.400, A:K.415, A:K.423, B:R.196 POP.7: 10 residues within 4Å: Chain A: R.196, D.313 Chain B: R.40, R.392, K.400, K.415, K.423 Ligands: MG.1, NMN.3, MG.5 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Water bridges: B:R.40, B:E.149, B:R.392, B:K.400, B:K.415, B:K.423, B:K.423, A:D.354 Salt bridges: B:R.40, B:R.392, B:K.400, B:K.400, B:K.415, B:K.423, A:R.196

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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