SMTL ID : 6tac.1

Human NAMPT deletion mutant in complex with nicotinamide mononucleotide, pyrophosphate, and Mg2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: G.124, F.125, V.126, R.436, F.442, N.481, A.482 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.126, A:R.436, A:R.436, A:N.481

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: R.52, R.394, K.425 Ligands: PPV.5 No protein-ligand interaction detected (PLIP) MG.3: 5 residues within 4Å: Chain A: H.249, R.313, D.315 Ligands: NMN.4, PPV.9 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.315, H2O.5 MG.6: 5 residues within 4Å: Chain B: R.52, R.394, K.425 Ligands: NMN.4, PPV.9 No protein-ligand interaction detected (PLIP) MG.7: 6 residues within 4Å: Chain A: K.425 Chain B: H.249, R.313, D.315 Ligands: PPV.5, NMN.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.315, H2O.25

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

NMN.4: 21 residues within 4Å: Chain A: F.195, R.198, G.199, D.221, A.246, H.249, R.313, D.315, G.355, D.356, S.384, G.385, G.386, G.387 Chain B: D.28, Y.30, R.394, K.425 Ligands: MG.3, MG.6, PPV.9 20 PLIP interactions: 12 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:F.195, B:Y.30, B:Y.30 Hydrogen bonds: A:D.221, A:R.313, A:R.313, A:D.315, A:G.385, A:G.386 Water bridges: A:D.356, A:G.357, A:V.358, A:G.387, B:R.394, B:R.394, B:D.395, B:D.395, B:K.425 pi-Stacking: A:F.195 Salt bridges: B:R.394 NMN.8: 20 residues within 4Å: Chain A: D.28, Y.30, R.394, K.425 Chain B: F.195, R.198, G.199, D.221, A.246, H.249, R.313, D.315, G.355, D.356, S.384, G.385, G.386, G.387 Ligands: PPV.5, MG.7 20 PLIP interactions: 12 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:F.195, A:Y.30, A:Y.30 Hydrogen bonds: B:D.221, B:R.313, B:R.313, B:D.315, B:G.355, B:G.385, B:G.386 Water bridges: B:G.357, B:V.358, B:S.384, A:R.394, A:R.394, A:R.394, A:R.394, A:K.425 pi-Stacking: B:F.195 Salt bridges: A:R.394

2 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.5: 11 residues within 4Å: Chain A: R.52, R.394, K.402, K.417, K.425 Chain B: R.198, H.249, D.315 Ligands: MG.2, MG.7, NMN.8 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B Water bridges: A:R.52, A:R.394, A:R.394, A:K.402, A:K.402, A:K.417, A:K.417, A:K.425, A:K.425, A:K.425, A:K.425, A:K.425, B:R.198 Salt bridges: A:R.52, A:R.394, A:K.402, A:K.402, A:K.417, A:K.425, B:R.198 PPV.9: 11 residues within 4Å: Chain A: R.198, H.249, D.315 Chain B: R.52, R.394, K.402, K.417, K.425 Ligands: MG.3, NMN.4, MG.6 19 PLIP interactions: 4 interactions with chain A, 15 interactions with chain B Water bridges: A:R.198, A:R.198, A:D.356, B:R.52, B:R.52, B:R.394, B:R.394, B:K.402, B:K.417, B:K.417, B:K.425, B:K.425 Salt bridges: A:R.198, B:R.52, B:R.394, B:K.402, B:K.402, B:K.417, B:K.425

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Houry, D. et al., Identification of structural determinants of NAMPT activity and substrate selectivity. To Be Published

Release Date

2020-11-18

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase