SMTL ID : 9iwt.2 (1 other biounit)

Crystal structure of human NAMPT complexed with AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 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: Y.18, R.392 Ligands: PO4.3, MG.4, PO4.6 20 PLIP interactions: 13 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:R.196, A:D.219, A:R.311, A:D.313, A:G.353, A:G.383, A:G.384 Water bridges: A:Y.195, A:D.313, A:G.385, A:G.385, B:R.392, B:R.392, B:D.393, B:K.400, B:K.415 pi-Stacking: A:F.193, A:F.193, B:Y.18 Salt bridges: B:R.392 AMP.5: 15 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, PO4.7, MG.8 11 PLIP interactions: 3 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:Y.18, B:D.219, B:R.311, B:D.313, B:G.353, B:G.383, B:G.384 Salt bridges: A:R.392 pi-Stacking: A:Y.18, B:F.193 Water bridges: B:Y.195

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

PO4.2: 6 residues within 4Å: Chain A: R.392, S.398, K.400 Chain B: R.196 Ligands: AMP.5, MG.8 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.40, A:S.398, B:R.196 Water bridges: A:E.149, A:F.399, A:K.415, A:K.415 Salt bridges: A:R.392, A:K.400 PO4.3: 7 residues within 4Å: Chain A: R.196, E.246, H.247, R.311, D.313 Chain B: Y.18 Ligands: AMP.1 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:Y.18, A:H.247 Water bridges: B:Y.18, B:E.149, B:K.400, B:K.400, A:R.196, A:R.196, A:S.248 Salt bridges: B:K.400, A:R.196, A:H.247, A:R.311 PO4.6: 5 residues within 4Å: Chain A: R.196 Chain B: R.392, S.398, K.400 Ligands: AMP.1 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.398, A:R.196 Water bridges: B:R.40, B:R.40, B:R.392, B:S.398, B:K.400, B:K.400, B:K.415, B:K.415 Salt bridges: B:R.392, B:K.400 PO4.7: 7 residues within 4Å: Chain A: Y.18 Chain B: R.196, E.246, H.247, R.311, D.313 Ligands: AMP.5 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain B Water bridges: A:E.149, B:R.196, B:R.196, B:R.196, B:E.246, B:S.248 Salt bridges: A:K.400, B:R.196, B:H.247, B:R.311 Hydrogen bonds: B:H.247

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.313, D.354 Chain B: K.423 Ligands: AMP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.354, H2O.18 MG.8: 3 residues within 4Å: Chain B: D.354 Ligands: PO4.2, AMP.5 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.354, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, G. et al., Crystal structure of human NAMPT complexed with AMP. To Be Published

Release Date

2025-06-11

Peptides

Nicotinamide phosphoribosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Nicotinamide phosphoribosyltransferase

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