SMTL ID : 2gvg.3 (3 other biounits)

Crystal Structure of human NMPRTase and its complex with NMN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 7 residues within 4Å: Chain A: R.196, E.246, H.247, R.311, D.313 Chain B: Y.18 Ligands: NMN.3 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:Y.18, B:Y.18, A:H.247 Water bridges: B:K.400, A:R.196, A:R.196, A:R.196, A:E.246, A:E.246, A:S.248 Salt bridges: A:R.196, A:H.247, A:R.311 PO4.2: 6 residues within 4Å: Chain A: R.392, S.398, K.400 Chain B: R.196 Ligands: PO4.5, NMN.6 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Water bridges: A:R.392, A:K.400, A:K.400, A:K.400, A:K.415, B:R.196, B:R.196, B:R.196 Salt bridges: A:R.392, A:K.400, B:R.196 PO4.4: 6 residues within 4Å: Chain A: G.197, G.384 Chain B: T.391, R.392, D.393 Ligands: NMN.3 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.384, B:T.391, B:T.391, B:R.392, B:D.393 Salt bridges: B:R.392 PO4.5: 8 residues within 4Å: Chain A: Y.18 Chain B: R.196, E.246, H.247, R.311, D.313 Ligands: PO4.2, NMN.6 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.247, A:Y.18 Water bridges: B:R.196, B:R.196, B:R.196, B:E.246, B:S.248, A:K.400 Salt bridges: B:R.196, B:H.247, B:R.311

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

NMN.3: 14 residues within 4Å: Chain A: F.193, R.196, D.219, R.311, D.313, G.353, D.354, G.383, G.384 Chain B: D.16, Y.18, R.392 Ligands: PO4.1, PO4.4 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.193, A:D.219, B:Y.18, B:Y.18 Hydrogen bonds: A:D.219, A:R.311, A:D.313, A:D.354, A:D.354, A:G.383, A:G.384 Water bridges: A:V.356, A:G.385 pi-Stacking: A:F.193 Salt bridges: B:R.392 NMN.6: 14 residues within 4Å: Chain A: D.16, Y.18, R.392 Chain B: F.193, R.196, D.219, R.311, D.313, G.353, D.354, G.383, G.384 Ligands: PO4.2, PO4.5 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:Y.18, A:Y.18, B:F.193 Water bridges: A:R.392, B:D.313 Salt bridges: A:R.392 Hydrogen bonds: B:D.219, B:R.311, B:R.311, B:D.313, B:D.354, B:G.383, B:G.384 pi-Stacking: B:F.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khan, J.A. et al., Molecular basis for the inhibition of human NMPRTase, a novel target for anticancer agents. Nat.Struct.Mol.Biol. (2006)

Release Date

2006-06-20

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

Nicotinamide phosphoribosyltransferase

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