SMTL ID : 6ta2.1

Human NAMPT in complex with nicotinic acid mononucleotide and phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-dimer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: G.134, F.135, V.136, R.446, F.452, N.491 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.136, A:R.446, A:R.446, A:N.491 Water bridges: A:N.491

2 x NCN: NICOTINATE MONONUCLEOTIDE(Non-covalent)

NCN.2: 17 residues within 4Å: Chain A: F.205, R.208, G.209, D.231, A.256, S.287, R.323, D.325, G.365, D.366, G.395, G.396 Chain B: D.28, Y.30, R.404 Ligands: PO4.5, CL.7 18 PLIP interactions: 11 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:F.205, B:Y.30, B:Y.30 Hydrogen bonds: A:D.325, A:G.365, A:G.395, A:G.396 Water bridges: A:R.323, A:R.323, A:R.323, A:G.397, B:R.404, B:R.404, B:K.435, B:K.435 Salt bridges: A:R.323, B:R.404 pi-Stacking: A:F.205 NCN.4: 17 residues within 4Å: Chain A: D.28, Y.30, R.404 Chain B: F.205, R.208, G.209, D.231, A.256, S.287, R.323, D.325, G.365, D.366, G.395, G.396 Ligands: PO4.3, CL.6 24 PLIP interactions: 13 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:F.205, B:D.231, A:Y.30, A:Y.30 Hydrogen bonds: B:R.323, B:D.325, B:G.365, B:G.395, B:G.396 Water bridges: B:R.323, B:D.366, B:D.366, B:D.366, A:R.404, A:R.404, A:R.404, A:R.404, A:R.404, A:R.404, A:R.404, A:K.435 Salt bridges: B:R.323, A:R.404 pi-Stacking: B:F.205

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

PO4.3: 8 residues within 4Å: Chain A: R.52, R.404, S.410, F.411, K.412, K.427, K.435 Ligands: NCN.4 21 PLIP interactions: 18 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.410, A:K.427 Water bridges: A:R.52, A:R.52, A:R.404, A:R.404, A:R.404, A:R.404, A:N.408, A:S.410, A:K.412, A:K.412, A:K.435, A:K.435, B:R.208, B:D.366, B:D.366 Salt bridges: A:R.52, A:R.404, A:K.412, A:K.435 PO4.5: 8 residues within 4Å: Chain B: R.52, R.404, S.410, F.411, K.412, K.427, K.435 Ligands: NCN.2 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:C.409, B:S.410, B:S.410, B:K.427 Water bridges: B:R.52, B:R.52, B:R.404, B:N.408, B:K.412, B:K.412, B:K.412, B:K.412, B:K.435, B:K.435, B:K.435, A:R.208 Salt bridges: B:R.52, B:R.404, B:K.412, B:K.435

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

CL.6: 5 residues within 4Å: Chain A: Y.30 Chain B: E.258, H.259, R.323 Ligands: NCN.4 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain A: R.208, E.258, H.259, R.323 Chain B: Y.30 Ligands: NCN.2 Ligand excluded by PLIP

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
B

B
A

Nicotinamide phosphoribosyltransferase

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