SMTL ID : 5eji.1

Crystal structure of NAD kinase W78F mutant from Listeria monocytogenes in complex with NADP/Mn++/PPi

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 24 residues within 4Å: Chain A: G.44, D.45, G.46, L.49, H.71, L.72, G.73, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222 Chain D: D.150, A.185, I.187, N.189, Y.192 Ligands: MN.2, POP.3 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:D.45, A:L.72, A:G.73, A:N.122, A:E.123, A:S.158, A:T.161, A:Y.163, A:S.166, D:A.185, D:N.189 pi-Stacking: A:Y.163 NAP.5: 24 residues within 4Å: Chain B: G.44, D.45, G.46, L.49, H.71, L.72, G.73, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222 Chain C: D.150, A.185, I.187, N.189, Y.192 Ligands: MN.6, POP.7 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:D.45, B:L.72, B:G.73, B:N.122, B:E.123, B:S.158, B:T.161, B:Y.163, B:S.166, C:A.185, C:N.189 pi-Stacking: B:Y.163 NAP.9: 24 residues within 4Å: Chain B: D.150, A.185, I.187, N.189, Y.192 Chain C: G.44, D.45, G.46, L.49, H.71, L.72, G.73, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222 Ligands: MN.10, POP.11 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:D.45, C:D.45, C:L.72, C:G.73, C:N.122, C:E.123, C:S.158, C:Y.163, C:S.166, B:A.185, B:N.189 pi-Stacking: C:Y.163 NAP.13: 24 residues within 4Å: Chain A: D.150, A.185, I.187, N.189, Y.192 Chain D: G.44, D.45, G.46, L.49, H.71, L.72, G.73, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222 Ligands: MN.14, POP.15 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:D.45, D:D.45, D:L.72, D:G.73, D:N.122, D:E.123, D:S.158, D:Y.163, D:S.166, A:A.185, A:N.189 pi-Stacking: D:Y.163

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 3 residues within 4Å: Chain A: G.46 Ligands: NAP.1, POP.3 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: POP.3 MN.6: 3 residues within 4Å: Chain B: G.46 Ligands: NAP.5, POP.7 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: POP.7 MN.10: 3 residues within 4Å: Chain C: G.46 Ligands: NAP.9, POP.11 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: POP.11 MN.14: 3 residues within 4Å: Chain D: G.46 Ligands: NAP.13, POP.15 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: POP.15

4 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.3: 7 residues within 4Å: Chain A: K.8, G.44, D.45, G.46, T.47 Ligands: NAP.1, MN.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.44, A:G.46, A:T.47, A:T.47, A:T.47, A:T.47 POP.7: 7 residues within 4Å: Chain B: K.8, G.44, D.45, G.46, T.47 Ligands: NAP.5, MN.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.44, B:G.46, B:T.47, B:T.47, B:T.47, B:T.47 POP.11: 7 residues within 4Å: Chain C: K.8, G.44, D.45, G.46, T.47 Ligands: NAP.9, MN.10 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.44, C:G.46, C:T.47, C:T.47, C:T.47 POP.15: 7 residues within 4Å: Chain D: K.8, G.44, D.45, G.46, T.47 Ligands: NAP.13, MN.14 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.44, D:G.46, D:T.47, D:T.47, D:T.47

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.4: 8 residues within 4Å: Chain A: Y.100, H.173, R.247, F.251, P.252, F.253 Chain C: H.204, H.205 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Y.100, A:F.253 Water bridges: A:F.251, A:F.251 Salt bridges: A:H.173, A:H.173, A:R.247, C:H.204, C:H.205 CIT.8: 8 residues within 4Å: Chain B: Y.100, H.173, R.247, F.251, P.252, F.253 Chain D: H.204, H.205 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:Y.100, B:F.253 Water bridges: B:F.251, B:F.251 Salt bridges: B:H.173, B:H.173, B:R.247, D:H.204, D:H.205 CIT.12: 8 residues within 4Å: Chain A: H.204, H.205 Chain C: Y.100, H.173, R.247, F.251, P.252, F.253 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:F.253 Water bridges: C:F.251, C:F.251 Salt bridges: C:H.173, C:H.173, C:R.247, A:H.204, A:H.205 CIT.16: 8 residues within 4Å: Chain B: H.204, H.205 Chain D: Y.100, H.173, R.247, F.251, P.252, F.253 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain D Salt bridges: B:H.204, B:H.205, D:H.173, D:H.173, D:R.247 Hydrogen bonds: D:F.253 Water bridges: D:F.251, D:F.251

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Poncet-Montange, G. et al., Crystal structure of NAD kinase W78F mutant from Listeria monocytogenes in complex with NADP/Mn++/PPi. to be published

Release Date

2016-11-09

Peptides

NAD kinase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

NAD kinase 1