SMTL ID : 8dsh.1

Human NAMPT in complex with quercitrin and AMPcP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x A12: PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

A12.1: 13 residues within 4Å: Chain A: F.193, R.196, A.244, R.311, G.353, G.381, S.382, G.383 Chain B: Y.18, R.40, R.392, S.398, K.400 25 PLIP interactions: 10 interactions with chain B, 15 interactions with chain A Hydrogen bonds: B:R.40, B:R.392, B:R.392, B:S.398, B:S.398, B:K.400, B:K.400, A:R.196, A:R.311, A:G.384 Water bridges: B:E.149, B:F.399, B:K.423, A:A.245, A:H.247, A:S.275, A:S.275, A:G.353, A:D.354, A:G.383, A:G.383 pi-Stacking: A:F.193, A:F.193 pi-Cation interactions: A:R.311, A:R.311 A12.3: 13 residues within 4Å: Chain A: Y.18, R.40, R.392, S.398, K.400 Chain B: F.193, R.196, A.244, R.311, G.353, S.382, G.383 Ligands: QCT.4 28 PLIP interactions: 10 interactions with chain A, 18 interactions with chain B Hydrogen bonds: A:Y.18, A:R.40, A:R.392, A:R.392, A:K.400, B:R.196, B:R.311 Water bridges: A:Y.18, A:N.396, A:C.397, A:F.399, A:K.400, B:F.193, B:R.196, B:A.245, B:S.275, B:S.275, B:S.275, B:R.311, B:R.311, B:G.353, B:S.382, B:G.383, B:G.384 pi-Stacking: B:F.193, B:F.193 pi-Cation interactions: B:R.311, B:R.311

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

QCT.2: 19 residues within 4Å: Chain A: Y.188, K.189, H.191, F.193, D.219, Y.240, S.241, V.242, A.244, P.273, P.307, I.309, R.349, V.350, I.351, E.376, N.377, I.378, A.379 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.242, A:P.273, A:P.307, A:I.309, A:R.349, A:I.351, A:A.379 Hydrogen bonds: A:K.189, A:V.242, A:E.376, A:N.377 Water bridges: A:V.242, A:R.349 QCT.4: 19 residues within 4Å: Chain B: Y.188, K.189, H.191, F.193, D.219, Y.240, S.241, V.242, P.273, P.307, I.309, R.349, V.350, I.351, E.376, N.377, I.378, A.379 Ligands: A12.3 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.242, B:P.273, B:P.307, B:R.349, B:I.351, B:A.379 Hydrogen bonds: B:K.189, B:S.241, B:V.242, B:R.349 Water bridges: B:K.189, B:H.191, B:E.376

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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