- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.56 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x CIT: CITRIC ACID(Non-functional Binders)
- 4 x KGX: 2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-[(2-azanylethylcarbamoylamino)methyl]-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]prop-2-ynyl]amino]ethanoic acid(Non-covalent)
KGX.2: 23 residues within 4Å:- Chain A: D.45, G.46, L.49, L.72, G.73, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222, H.223
- Chain D: P.132, G.149, D.150, A.185, I.187, N.189, Y.192
17 PLIP interactions:13 interactions with chain A, 4 interactions with chain D- Hydrophobic interactions: A:D.45, A:L.49
- Hydrogen bonds: A:G.73, A:N.122, A:S.158, A:T.161, A:Y.163, A:S.166, D:A.185, D:N.189
- Water bridges: A:D.45, A:D.45, A:H.71, D:F.133, D:Y.192
- Salt bridges: A:H.223
- pi-Stacking: A:Y.163
KGX.4: 23 residues within 4Å:- Chain B: D.45, G.46, L.49, L.72, G.73, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222, H.223
- Chain C: P.132, G.149, D.150, A.185, I.187, N.189, Y.192
17 PLIP interactions:13 interactions with chain B, 4 interactions with chain C- Hydrophobic interactions: B:D.45, B:L.49
- Hydrogen bonds: B:G.73, B:N.122, B:S.158, B:T.161, B:Y.163, B:S.166, C:A.185, C:N.189
- Water bridges: B:D.45, B:D.45, B:H.71, C:F.133, C:Y.192
- Salt bridges: B:H.223
- pi-Stacking: B:Y.163
KGX.6: 23 residues within 4Å:- Chain B: P.132, G.149, D.150, A.185, I.187, N.189, Y.192
- Chain C: D.45, G.46, L.49, L.72, G.73, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222, H.223
17 PLIP interactions:3 interactions with chain B, 14 interactions with chain C- Hydrogen bonds: B:A.185, B:N.189, C:D.45, C:G.73, C:Y.75, C:N.122, C:S.158, C:Y.163, C:S.166
- Water bridges: B:F.133, C:D.45, C:D.45, C:H.71
- Hydrophobic interactions: C:D.45, C:L.49
- Salt bridges: C:H.223
- pi-Stacking: C:Y.163
KGX.8: 23 residues within 4Å:- Chain A: P.132, G.149, D.150, A.185, I.187, N.189, Y.192
- Chain D: D.45, G.46, L.49, L.72, G.73, F.74, Y.75, N.122, E.123, S.158, T.161, A.162, Y.163, S.166, D.222, H.223
17 PLIP interactions:14 interactions with chain D, 3 interactions with chain A- Hydrophobic interactions: D:D.45, D:L.49
- Hydrogen bonds: D:D.45, D:G.73, D:Y.75, D:N.122, D:S.158, D:Y.163, D:S.166, A:A.185, A:N.189
- Water bridges: D:D.45, D:D.45, D:H.71, A:F.133
- Salt bridges: D:H.223
- pi-Stacking: D:Y.163
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Clement, D.A. et al., Synthesis and structure-activity relationship studies of original cyclic diadenosine derivatives as nanomolar inhibitors of NAD kinase from pathogenic bacteria. Eur.J.Med.Chem. (2023)
- Release Date
- 2023-01-11
- Peptides
- NAD kinase 1: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
AD
A
SMTL ID : 7zzb.1
Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a linear di-adenosine derivative
NAD kinase 1
Toggle Identical (ABCD)Related Entries With Identical Sequence
2i1w.1 | 2i29.1 | 2i2a.1 | 2i2b.1 | 2i2c.1 | 2i2d.1 | 2i2e.1 | 3v7u.1 | 3v7w.1 | 3v7y.1 | 3v80.1 | 3v8m.1 | 3v8n.1 | 3v8p.1 | 4dy6.1 | 5dhp.1 | 5dhq.1 | 5dhr.1 | 5dhs.1 | 5dht.1 | 5dhu.1 | 6rbo.1 | 6rbp.1 | 6rbq.1 | 6rbr.1 | 6rbs.1 | 6rbt.1 | 6rbu.1 | 6rbv.1 | 6rbw.1 more...less...6rbx.1 | 6rby.1 | 6rbz.1 | 6rc0.1 | 6rc1.1 | 6rc2.1 | 6rc3.1 | 6rc4.1 | 6rc5.1 | 6rc6.1 | 6rg6.1 | 6rg7.1 | 6rg8.1 | 6rg9.1 | 6rga.1 | 6rgb.1 | 6rgc.1 | 6rgd.1 | 6rge.1 | 6rgf.1 | 6rr2.1 | 6z61.1 | 6z64.1 | 6z65.1 | 7zz7.1 | 7zz9.1 | 7zza.1 | 7zzc.1 | 7zzd.1 | 7zze.1 | 7zzf.1 | 7zzg.1 | 7zzh.1 | 7zzj.1 | 8a9v.1 | 8b47.1