SMTL ID : 3v8p.1

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a new di-adenosine inhibitor formed in situ

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-tetramer

Ligands

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

CIT.1: 9 residues within 4Å: Chain A: V.98, Y.100, H.173, P.174, 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.3: 9 residues within 4Å: Chain B: V.98, Y.100, H.173, P.174, 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.5: 9 residues within 4Å: Chain C: V.98, Y.100, H.173, P.174, 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.7: 9 residues within 4Å: Chain D: V.98, Y.100, H.173, P.174, 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 ZNB: 2-[6-azanyl-9-[(2R,3R,4S,5R)-5-[[(azanylidene-$l^{4}-azanylidene)amino]methyl]-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]sulfanyl-N-[[(2R,3S,4R,5R)-5-(6-azanyl-8-bromanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]ethanamide(Non-covalent)

ZNB.2: 18 residues within 4Å: Chain A: D.45, G.46, L.49, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222 Chain D: G.149, D.150, A.185, I.187, N.189 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:N.122, A:E.123, A:S.158, A:T.161, A:Y.163, A:S.166, A:D.222, D:A.185, D:N.189 Water bridges: A:D.45, D:N.189 pi-Stacking: A:Y.163 ZNB.4: 18 residues within 4Å: Chain B: D.45, G.46, L.49, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222 Chain C: G.149, D.150, A.185, I.187, N.189 12 PLIP interactions: 3 interactions with chain C, 9 interactions with chain B Hydrogen bonds: C:A.185, C:N.189, B:N.122, B:E.123, B:S.158, B:T.161, B:Y.163, B:S.166, B:D.222 Water bridges: C:N.189, B:D.45 pi-Stacking: B:Y.163 ZNB.6: 18 residues within 4Å: Chain B: G.149, D.150, A.185, I.187, N.189 Chain C: D.45, G.46, L.49, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:D.45, C:N.122, C:E.123, C:S.158, C:Y.163, C:S.166, C:D.222, B:A.185, B:N.189 Water bridges: C:D.45, C:T.161, B:N.189 pi-Stacking: C:Y.163 ZNB.8: 18 residues within 4Å: Chain A: G.149, D.150, A.185, I.187, N.189 Chain D: D.45, G.46, L.49, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain D Hydrogen bonds: A:A.185, A:N.189, D:D.45, D:N.122, D:E.123, D:S.158, D:Y.163, D:S.166, D:D.222 Water bridges: A:N.189, D:D.45, D:T.161 pi-Stacking: D:Y.163

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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