SMTL ID : 6ta0.1

Human NAMPT in complex with nicotinic acid and phosphoribosyl pyrophosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-dimer

Ligands

2 x PRP: 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose(Non-covalent)

PRP.1: 20 residues within 4Å: Chain A: F.205, R.208, H.259, R.323, D.325, G.365, D.366, S.394, G.395, G.396, G.397 Chain B: Y.30, R.52, R.404, C.409, S.410, K.412, K.427, K.435 Ligands: NIO.4 38 PLIP interactions: 12 interactions with chain A, 26 interactions with chain B Hydrogen bonds: A:R.323, A:R.323, A:D.325, A:D.366, A:G.395, A:G.396, B:S.410 Water bridges: A:R.208, A:G.367, A:G.367, A:G.397, B:R.52, B:R.52, B:E.161, B:E.161, B:R.404, B:R.404, B:R.404, B:R.404, B:R.404, B:R.404, B:R.404, B:R.404, B:K.412, B:K.427, B:K.427, B:K.427, B:K.435, B:K.435 Salt bridges: A:R.208, A:R.208, B:R.52, B:R.404, B:R.404, B:R.404, B:R.404, B:K.412, B:K.412 PRP.3: 18 residues within 4Å: Chain A: R.52, R.404, S.410, K.412, K.427, K.435 Chain B: F.205, R.208, H.259, R.323, D.325, G.365, D.366, S.394, G.395, G.396, G.397 Ligands: NIO.6 32 PLIP interactions: 11 interactions with chain B, 21 interactions with chain A Hydrogen bonds: B:R.323, B:R.323, B:G.365, B:G.395, B:G.396 Water bridges: B:R.208, B:R.208, B:G.367, B:G.397, A:R.52, A:R.404, A:R.404, A:R.404, A:R.404, A:R.404, A:R.404, A:F.411, A:K.412, A:K.412, A:K.427, A:K.427, A:K.435, A:K.435 Salt bridges: B:R.208, B:R.208, A:R.52, A:R.404, A:R.404, A:R.404, A:R.404, A:K.412, A:K.412

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: G.134, F.135, V.136, I.137, R.446, F.452, N.491, A.492 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.136, A:V.136, A:R.446, A:N.491 GOL.5: 7 residues within 4Å: Chain B: G.134, F.135, V.136, I.137, R.446, F.452, N.491 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.136, B:V.136, B:R.446, B:N.491

2 x NIO: NICOTINIC ACID(Non-covalent)

NIO.4: 9 residues within 4Å: Chain A: F.205, R.208, D.231, A.256, S.287, R.323 Chain B: D.28, Y.30 Ligands: PRP.1 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.205, A:D.231 Hydrogen bonds: A:D.231 Water bridges: A:R.323 Salt bridges: A:R.323 pi-Stacking: A:F.205, B:Y.30 NIO.6: 9 residues within 4Å: Chain A: D.28, Y.30 Chain B: F.205, R.208, D.231, A.256, S.287, R.323 Ligands: PRP.3 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.205, B:D.231 Hydrogen bonds: B:D.231 Water bridges: B:R.323 Salt bridges: B:R.323 pi-Stacking: B:F.205, A:Y.30

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

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