SMTL ID : 3v7u.1

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with MTA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-tetramer

Ligands

8 x MTA: 5'-DEOXY-5'-METHYLTHIOADENOSINE(Non-covalent)

MTA.1: 9 residues within 4Å: Chain A: D.45, F.74, Y.75, N.122, S.158, T.161, A.162 Chain D: Y.192 Ligands: MTA.2 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.122, A:S.158, A:T.161 Water bridges: D:N.189 MTA.2: 13 residues within 4Å: Chain A: D.45, G.46, L.49, N.122, E.123, A.162, Y.163, S.166, D.222 Chain D: G.149, D.150, A.185 Ligands: MTA.1 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.122, A:E.123, A:Y.163, A:S.166, A:D.222, D:A.185 pi-Stacking: A:Y.163 MTA.5: 9 residues within 4Å: Chain B: D.45, F.74, Y.75, N.122, S.158, T.161, A.162 Chain C: Y.192 Ligands: MTA.6 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.122, B:S.158, B:T.161 Water bridges: C:N.189 MTA.6: 13 residues within 4Å: Chain B: D.45, G.46, L.49, N.122, E.123, A.162, Y.163, S.166, D.222 Chain C: G.149, D.150, A.185 Ligands: MTA.5 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.122, B:E.123, B:Y.163, B:S.166, B:D.222, C:A.185 pi-Stacking: B:Y.163 MTA.9: 9 residues within 4Å: Chain B: Y.192 Chain C: D.45, F.74, Y.75, N.122, S.158, T.161, A.162 Ligands: MTA.10 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Water bridges: B:N.189 Hydrogen bonds: C:D.45, C:N.122, C:S.158 MTA.10: 13 residues within 4Å: Chain B: G.149, D.150, A.185 Chain C: D.45, G.46, L.49, N.122, E.123, A.162, Y.163, S.166, D.222 Ligands: MTA.9 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:A.185, C:N.122, C:E.123, C:Y.163, C:S.166, C:D.222 pi-Stacking: C:Y.163 MTA.13: 9 residues within 4Å: Chain A: Y.192 Chain D: D.45, F.74, Y.75, N.122, S.158, T.161, A.162 Ligands: MTA.14 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:D.45, D:N.122, D:S.158 Water bridges: A:N.189 MTA.14: 13 residues within 4Å: Chain A: G.149, D.150, A.185 Chain D: D.45, G.46, L.49, N.122, E.123, A.162, Y.163, S.166, D.222 Ligands: MTA.13 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:N.122, D:E.123, D:Y.163, D:S.166, D:D.222, A:A.185 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 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.98 Hydrogen bonds: A:Y.100, A:F.253 Salt bridges: A:H.173, A:H.173, A:R.247, A:R.256 CIT.7: 8 residues within 4Å: Chain B: V.98, Y.100, H.173, R.247, F.251, P.252, F.253, R.256 7 PLIP interactions: 7 interactions with chain B 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 CIT.11: 8 residues within 4Å: Chain C: V.98, Y.100, H.173, R.247, F.251, P.252, F.253, R.256 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.98 Hydrogen bonds: C:F.253 Salt bridges: C:H.173, C:H.173, C:R.247, C:R.256 CIT.15: 8 residues within 4Å: Chain D: V.98, Y.100, H.173, R.247, F.251, P.252, F.253, R.256 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.98 Hydrogen bonds: D:F.253 Salt bridges: D:H.173, D:H.173, D:R.247, D:R.256

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: K.8, G.44, D.45, G.46, T.47 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 Water bridges: A:D.45 GOL.8: 5 residues within 4Å: Chain B: K.8, G.44, D.45, G.46, T.47 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 Water bridges: B:D.45 GOL.12: 5 residues within 4Å: Chain C: K.8, G.44, D.45, G.46, T.47 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.44, C:G.46, C:T.47, C:T.47 Water bridges: C:D.45 GOL.16: 5 residues within 4Å: Chain D: K.8, G.44, D.45, G.46, T.47 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.44, D:G.46, D:T.47, D:T.47 Water bridges: D:D.45

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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