SMTL ID : 3dhf.1

Crystal structure of phosphorylated mimic form of human NAMPT complexed with nicotinamide mononucleotide and pyrophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.313 Ligands: NMN.3, BEF.4, POP.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.313 MG.2: 4 residues within 4Å: Chain A: R.40, R.392, K.423 Ligands: POP.5 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain B: R.40, R.392, K.423 Ligands: POP.8 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: D.313 Ligands: POP.5, NMN.9, BEF.10 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.313

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

NMN.3: 17 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, BEF.4, POP.8 19 PLIP interactions: 10 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:G.383, A:G.384, B:D.393 Water bridges: A:D.354, A:G.355, A:G.385, B:R.392, B:R.392, B:R.392, B:D.393, B:K.423 pi-Stacking: A:F.193 Salt bridges: B:R.392 NMN.9: 16 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.5, MG.7, BEF.10 20 PLIP interactions: 10 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:Y.18, A:Y.18, B:F.193 Hydrogen bonds: A:D.393, B:D.219, B:R.311, B:R.311, B:G.383, B:G.384 Water bridges: A:R.392, A:R.392, A:R.392, A:R.392, A:K.423, A:K.423, B:G.355, B:V.356, B:G.385 Salt bridges: A:R.392 pi-Stacking: B:F.193

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Covalent)

BEF.4: 8 residues within 4Å: Chain A: E.246, H.247, D.313 Chain B: K.400, K.415 Ligands: MG.1, NMN.3, POP.8 No protein-ligand interaction detected (PLIP) BEF.10: 8 residues within 4Å: Chain A: K.400, K.415 Chain B: E.246, H.247, D.313 Ligands: POP.5, MG.7, NMN.9 No protein-ligand interaction detected (PLIP)

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

POP.5: 11 residues within 4Å: Chain A: R.40, R.392, K.400, K.415, K.423 Chain B: R.196, D.313 Ligands: MG.2, MG.7, NMN.9, BEF.10 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Water bridges: A:R.40, A:E.149, A:R.392, A:R.392, A:K.400, A:K.415, A:K.423, A:K.423 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.400, A:K.415, A:K.423, A:K.423, B:R.196 POP.8: 11 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, BEF.4, MG.6 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A Water bridges: B:R.392, B:R.392, B:R.392, B:K.415, B:K.423, B:K.423, A:D.313, A:D.354 Salt bridges: B:R.40, B:R.392, B:K.400, B:K.400, B:K.415, B:K.423, 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

Related Entries With Identical Sequence