SMTL ID : 3v7y.1

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 5'-N-Propargylamino-5'-deoxyadenosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-tetramer

Ligands

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

CIT.1: 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: 8 interactions with chain A Hydrophobic interactions: A:V.98 Hydrogen bonds: A:Y.100, A:F.253 Water bridges: A:W.254 Salt bridges: A:H.173, A:H.173, A:R.247, A:R.256 CIT.4: 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: 8 interactions with chain B Hydrophobic interactions: B:V.98 Hydrogen bonds: B:Y.100, B:F.253 Water bridges: B:W.254 Salt bridges: B:H.173, B:H.173, B:R.247, B:R.256 CIT.7: 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: 7 interactions with chain C Hydrophobic interactions: C:V.98 Hydrogen bonds: C:F.253 Water bridges: C:W.254 Salt bridges: C:H.173, C:H.173, C:R.247, C:R.256 CIT.10: 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: 7 interactions with chain D Hydrophobic interactions: D:V.98 Hydrogen bonds: D:F.253 Water bridges: D:W.254 Salt bridges: D:H.173, D:H.173, D:R.247, D:R.256

8 x A3N: 5'-deoxy-5'-(prop-2-yn-1-ylamino)adenosine(Non-covalent)

A3N.2: 13 residues within 4Å: Chain A: G.46, L.49, N.122, E.123, A.162, Y.163, S.166, D.222 Chain D: G.149, D.150, A.185, I.187 Ligands: A3N.3 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:L.49 Hydrogen bonds: A:N.122, A:E.123, A:Y.163, A:S.166, D:A.185 pi-Stacking: A:Y.163 A3N.3: 10 residues within 4Å: Chain A: D.45, H.71, F.74, Y.75, N.122, S.158, T.161, A.162 Chain D: I.187 Ligands: A3N.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.75, A:N.122, A:S.158, A:T.161 Water bridges: A:D.45, A:H.71 A3N.5: 13 residues within 4Å: Chain B: G.46, L.49, N.122, E.123, A.162, Y.163, S.166, D.222 Chain C: G.149, D.150, A.185, I.187 Ligands: A3N.6 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain B Hydrogen bonds: C:A.185, B:N.122, B:E.123, B:Y.163, B:S.166 Hydrophobic interactions: B:L.49 pi-Stacking: B:Y.163 A3N.6: 10 residues within 4Å: Chain B: D.45, H.71, F.74, Y.75, N.122, S.158, T.161, A.162 Chain C: I.187 Ligands: A3N.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.75, B:N.122, B:S.158, B:T.161 Water bridges: B:D.45, B:H.71 A3N.8: 13 residues within 4Å: Chain B: G.149, D.150, A.185, I.187 Chain C: G.46, L.49, N.122, E.123, A.162, Y.163, S.166, D.222 Ligands: A3N.9 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.49 Hydrogen bonds: C:N.122, C:E.123, C:Y.163, C:S.166, B:A.185 pi-Stacking: C:Y.163 A3N.9: 10 residues within 4Å: Chain B: I.187 Chain C: D.45, H.71, F.74, Y.75, N.122, S.158, T.161, A.162 Ligands: A3N.8 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.45, C:N.122, C:S.158 Water bridges: C:D.45, C:H.71, C:T.161 A3N.11: 13 residues within 4Å: Chain A: G.149, D.150, A.185, I.187 Chain D: G.46, L.49, N.122, E.123, A.162, Y.163, S.166, D.222 Ligands: A3N.12 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:L.49 Hydrogen bonds: D:N.122, D:E.123, D:Y.163, D:S.166, A:A.185 pi-Stacking: D:Y.163 A3N.12: 10 residues within 4Å: Chain A: I.187 Chain D: D.45, H.71, F.74, Y.75, N.122, S.158, T.161, A.162 Ligands: A3N.11 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.45, D:N.122, D:S.158 Water bridges: D:D.45, D:H.71, D:T.161

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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