SMTL ID : 2i2b.1

Crystal structure of LmNADK1 from Listeria monocytogenes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

8 x CC5: BETA-D-ERYTHROFURANOSYL-ADENOSINE(Non-covalent)

CC5.1: 13 residues within 4Å: Chain A: L.49, N.122, E.123, A.162, Y.163, S.166, D.222 Chain D: P.132, G.149, D.150, A.185, I.187 Ligands: CC5.2 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain A Hydrogen bonds: D:A.185, A:N.122, A:E.123, A:Y.163, A:S.166 pi-Stacking: A:Y.163 CC5.2: 9 residues within 4Å: Chain A: D.45, F.74, Y.75, N.122, S.158, T.161, A.162 Chain D: R.148 Ligands: CC5.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.122, A:S.158, A:T.161, D:R.148 CC5.5: 13 residues within 4Å: Chain B: L.49, N.122, E.123, A.162, Y.163, S.166, D.222 Chain C: P.132, G.149, D.150, A.185, I.187 Ligands: CC5.6 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.122, B:E.123, B:Y.163, B:S.166, C:A.185 pi-Stacking: B:Y.163 CC5.6: 9 residues within 4Å: Chain B: D.45, F.74, Y.75, N.122, S.158, T.161, A.162 Chain C: R.148 Ligands: CC5.5 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.122, B:S.158, B:T.161, C:R.148 CC5.9: 13 residues within 4Å: Chain B: P.132, G.149, D.150, A.185, I.187 Chain C: L.49, N.122, E.123, A.162, Y.163, S.166, D.222 Ligands: CC5.10 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:A.185, C:N.122, C:E.123, C:Y.163, C:S.166 pi-Stacking: C:Y.163 CC5.10: 9 residues within 4Å: Chain B: R.148 Chain C: D.45, F.74, Y.75, N.122, S.158, T.161, A.162 Ligands: CC5.9 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Y.75, C:N.122, C:S.158, B:R.148 Water bridges: C:T.161 CC5.13: 13 residues within 4Å: Chain A: P.132, G.149, D.150, A.185, I.187 Chain D: L.49, N.122, E.123, A.162, Y.163, S.166, D.222 Ligands: CC5.14 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:N.122, D:E.123, D:Y.163, D:S.166, A:A.185 pi-Stacking: D:Y.163 CC5.14: 9 residues within 4Å: Chain A: R.148 Chain D: D.45, F.74, Y.75, N.122, S.158, T.161, A.162 Ligands: CC5.13 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:Y.75, D:N.122, D:S.158, A:R.148 Water bridges: D:T.161

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

CIT.3: 8 residues within 4Å: Chain A: V.98, Y.100, H.173, R.247, F.251, P.252, F.253, R.256 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain A Salt bridges: C:H.205, A:H.173, A:H.173, A:R.247, A:R.256 Hydrophobic interactions: A:V.98 Hydrogen bonds: A:Y.100, A:F.253 CIT.7: 8 residues within 4Å: Chain B: V.98, Y.100, H.173, R.247, F.251, P.252, F.253, R.256 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:V.98 Hydrogen bonds: B:Y.100, B:F.253 Salt bridges: B:H.173, B:H.173, B:R.247, B:R.256, D:H.205 CIT.11: 8 residues within 4Å: Chain C: V.98, Y.100, H.173, R.247, F.251, P.252, F.253, R.256 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.98 Hydrogen bonds: C:F.253 Salt bridges: C:H.173, C:H.173, C:R.247, C:R.256, A:H.205 CIT.15: 8 residues within 4Å: Chain D: V.98, Y.100, H.173, R.247, F.251, P.252, F.253, R.256 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:V.98 Hydrogen bonds: D:F.253 Salt bridges: D:H.173, D:H.173, D:R.247, D:R.256, B:H.205

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: W.254, R.255, H.258 Chain C: I.139, I.142, H.143, F.144 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.139, C:I.139 Water bridges: C:N.140 GOL.8: 7 residues within 4Å: Chain B: W.254, R.255, H.258 Chain D: I.139, I.142, H.143, F.144 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:I.139, D:I.139 Water bridges: D:N.140 GOL.12: 7 residues within 4Å: Chain A: I.139, I.142, H.143, F.144 Chain C: W.254, R.255, H.258 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:H.258, A:I.139, A:I.139 Water bridges: A:N.140 GOL.16: 7 residues within 4Å: Chain B: I.139, I.142, H.143, F.144 Chain D: W.254, R.255, H.258 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:I.139, B:I.139, D:H.258 Water bridges: B:N.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Poncet-Montange, G. et al., NAD kinases use substrate-assisted catalysis for specific recognition of NAD. J.Biol.Chem. (2007)

Release Date

2007-08-07

Peptides

Probable inorganic polyphosphate/ATP-NAD kinase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Probable inorganic polyphosphate/ATP-NAD kinase 1

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