SMTL ID : 3v8n.1

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 8-bromo-5'-amino-5'-deoxyadenosine, reacted with a citrate molecule in N site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-tetramer

Ligands

4 x 5NB: 5'-amino-8-bromo-5'-deoxyadenosine(Non-covalent)

5NB.1: 14 residues within 4Å: Chain A: D.45, G.46, L.49, L.72, G.73, F.74, Y.75, N.122, S.158, T.161, A.162 Chain D: I.187, N.189 Ligands: 5CI.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.72, A:N.122, A:S.158, A:T.161 Water bridges: A:D.45, A:D.45, A:G.46 5NB.4: 14 residues within 4Å: Chain B: D.45, G.46, L.49, L.72, G.73, F.74, Y.75, N.122, S.158, T.161, A.162 Chain C: I.187, N.189 Ligands: 5CI.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:L.72, B:N.122, B:S.158, B:T.161 Water bridges: B:D.45, B:D.45, B:G.46 5NB.7: 14 residues within 4Å: Chain B: I.187, N.189 Chain C: D.45, G.46, L.49, L.72, G.73, F.74, Y.75, N.122, S.158, T.161, A.162 Ligands: 5CI.8 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.45, C:L.72, C:Y.75, C:N.122, C:S.158 Water bridges: C:D.45, C:D.45, C:G.46 5NB.10: 14 residues within 4Å: Chain A: I.187, N.189 Chain D: D.45, G.46, L.49, L.72, G.73, F.74, Y.75, N.122, S.158, T.161, A.162 Ligands: 5CI.11 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:D.45, D:L.72, D:Y.75, D:N.122, D:S.158 Water bridges: D:D.45, D:D.45, D:G.46

4 x 5CI: 8-bromo-5'-{[3-carboxy-2-(carboxymethyl)-2-hydroxypropanoyl]amino}-5'-deoxyadenosine(Non-covalent)

5CI.2: 15 residues within 4Å: Chain A: G.46, T.47, L.49, N.122, E.123, A.162, Y.163, S.166, D.222 Chain D: R.148, G.149, D.150, A.185, I.187 Ligands: 5NB.1 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:N.122, A:E.123, A:Y.163, A:S.166, A:D.222, D:R.148, D:A.185 Water bridges: A:G.46, A:T.47, A:S.50, A:S.50 pi-Stacking: A:Y.163 Salt bridges: D:R.148 5CI.5: 15 residues within 4Å: Chain B: G.46, T.47, L.49, N.122, E.123, A.162, Y.163, S.166, D.222 Chain C: R.148, G.149, D.150, A.185, I.187 Ligands: 5NB.4 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:N.122, B:E.123, B:Y.163, B:S.166, B:D.222, C:R.148, C:A.185 Water bridges: B:G.46, B:T.47, B:S.50, B:S.50 pi-Stacking: B:Y.163 Salt bridges: C:R.148 5CI.8: 15 residues within 4Å: Chain B: R.148, G.149, D.150, A.185, I.187 Chain C: G.46, T.47, L.49, N.122, E.123, A.162, Y.163, S.166, D.222 Ligands: 5NB.7 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain C Hydrogen bonds: B:R.148, B:A.185, C:N.122, C:E.123, C:Y.163, C:S.166, C:D.222 Salt bridges: B:R.148 Water bridges: C:G.46, C:T.47, C:S.50, C:S.50 pi-Stacking: C:Y.163 5CI.11: 15 residues within 4Å: Chain A: R.148, G.149, D.150, A.185, I.187 Chain D: G.46, T.47, L.49, N.122, E.123, A.162, Y.163, S.166, D.222 Ligands: 5NB.10 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain D Hydrogen bonds: A:R.148, A:A.185, D:N.122, D:E.123, D:Y.163, D:S.166, D:D.222 Salt bridges: A:R.148 Water bridges: D:G.46, D:T.47, D:S.50, D:S.50 pi-Stacking: D:Y.163

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 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.98 Hydrogen bonds: A:Y.100, A:F.253 Water bridges: A:R.247, A:R.247 Salt bridges: A:H.173, A:H.173, A:R.247, A:R.256, C:H.205 CIT.6: 8 residues within 4Å: Chain B: V.98, Y.100, H.173, R.247, F.251, P.252, F.253, R.256 10 PLIP interactions: 1 interactions with chain D, 9 interactions with chain B Salt bridges: D:H.205, B:H.173, B:H.173, B:R.247, B:R.256 Hydrophobic interactions: B:V.98 Hydrogen bonds: B:Y.100, B:F.253 Water bridges: B:R.247, B:R.247 CIT.9: 8 residues within 4Å: Chain C: V.98, Y.100, H.173, R.247, F.251, P.252, F.253, R.256 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.98 Hydrogen bonds: C:F.253 Water bridges: C:R.247, C:R.247 Salt bridges: C:H.173, C:H.173, C:R.247, C:R.256, A:H.205 CIT.12: 8 residues within 4Å: Chain D: V.98, Y.100, H.173, R.247, F.251, P.252, F.253, R.256 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:V.98 Hydrogen bonds: D:F.253 Water bridges: D:R.247, D:R.247 Salt bridges: D:H.173, D:H.173, D:R.247, D:R.256, B:H.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gelin, M. et al., Screening and In Situ Synthesis Using Crystals of a NAD Kinase Lead to a Potent Antistaphylococcal Compound. Structure (2012)

Release Date

2012-03-14

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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