SMTL ID : 8dse.1

Human NAMPT in complex with substrate NAM and activator quercitrin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-dimer

Ligands

2 x NCA: NICOTINAMIDE(Non-covalent)

NCA.1: 8 residues within 4Å: Chain A: F.193, R.196, D.219, A.244, R.311 Chain B: D.16, Y.18 Ligands: QCT.5 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.193, A:D.219, B:Y.18 Hydrogen bonds: A:D.219 pi-Stacking: A:F.193 NCA.7: 8 residues within 4Å: Chain A: D.16, Y.18 Chain B: F.193, R.196, D.219, A.244, R.311 Ligands: QCT.9 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.18, B:F.193, B:D.219 Hydrogen bonds: B:D.219 pi-Stacking: B:F.193

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

CL.2: 3 residues within 4Å: Chain A: K.73, T.76, K.77 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: E.246, R.311 Chain B: Y.18 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: Y.18 Chain B: E.246, R.311 Ligand excluded by PLIP

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

PO4.3: 6 residues within 4Å: Chain A: R.40, R.392, C.397, S.398, K.400, K.423 12 PLIP interactions: 12 interactions with chain A Water bridges: A:R.40, A:R.40, A:R.392, A:K.400, A:K.400, A:K.400, A:K.400, A:K.415 Salt bridges: A:R.40, A:R.392, A:K.400, A:K.415 PO4.8: 6 residues within 4Å: Chain B: R.40, R.392, C.397, S.398, K.400, K.423 14 PLIP interactions: 3 interactions with chain A, 11 interactions with chain B Water bridges: A:D.313, A:D.313, A:D.354, B:R.40, B:R.40, B:R.392, B:R.392, B:K.400, B:K.415 Hydrogen bonds: B:S.398 Salt bridges: B:R.40, B:R.392, B:K.400, B:K.415

2 x QCT: 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-chromen-3-yl 6-deoxy-alpha-L-mannopyranoside(Non-covalent)

QCT.5: 16 residues within 4Å: Chain A: Y.188, K.189, H.191, Y.240, S.241, V.242, P.307, I.309, R.349, V.350, I.351, E.376, N.377, I.378, A.379 Ligands: NCA.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.242, A:P.307, A:R.349, A:I.351, A:A.379 Hydrogen bonds: A:K.189, A:K.189 QCT.9: 16 residues within 4Å: Chain B: Y.188, K.189, H.191, Y.240, S.241, V.242, P.307, I.309, R.349, V.350, I.351, E.376, N.377, I.378, A.379 Ligands: NCA.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.242, B:P.307, B:I.309, B:I.309, B:R.349, B:I.351, B:A.379 Hydrogen bonds: B:K.189 Water bridges: B:H.191

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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