SMTL ID : 8dsi.1

Human NAMPT in complex with substrate NAM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-dimer

Ligands

2 x NCA: NICOTINAMIDE(Non-covalent)

NCA.1: 7 residues within 4Å: Chain A: F.193, R.196, D.219, A.244, R.311 Chain B: D.16, Y.18 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 NCA.6: 7 residues within 4Å: Chain A: D.16, Y.18 Chain B: F.193, R.196, D.219, A.244, R.311 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

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 6 residues within 4Å: Chain A: R.40, R.392, C.397, S.398, K.400, K.423 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.398 Water bridges: A:R.40, A:R.392, A:K.400, A:K.400, A:K.400, A:K.400, A:K.415, A:K.415, A:K.415 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.415 PO4.7: 6 residues within 4Å: Chain B: R.40, R.392, C.397, S.398, K.400, K.423 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:C.397 Water bridges: B:R.392, B:K.400, B:K.400, B:K.400, B:K.415, B:K.423, A:D.354 Salt bridges: B:R.40, B:R.392, B:K.400, B:K.415, B:K.423

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: N.29, T.30, P.139, E.140 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.29, A:N.29, A:E.140, A:E.140 Water bridges: A:E.140

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: K.73, T.76, K.77 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: E.246, R.311 Chain B: Y.18 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: Y.18 Chain B: E.246, R.311 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ratia, K.M. et al., Mechanism of Allosteric Modulation of Nicotinamide Phosphoribosyltransferase to Elevate Cellular NAD. Biochemistry (2023)

Release Date

2023-03-08

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nicotinamide phosphoribosyltransferase

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