SMTL ID : 8qw2.1

Human NDPK-C in complex with UDP and Mg2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-hexamer

Ligands

6 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.1: 13 residues within 4Å: Chain A: K.15, L.58, R.61, F.63, L.67, R.91, T.97, R.108, V.115, G.116, N.118 Chain B: E.155 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.115 Hydrogen bonds: A:K.15, A:R.61, A:T.97, A:R.108, A:R.108, A:V.115, A:N.118, A:N.118, A:H.121 Water bridges: A:R.91, A:G.122 Salt bridges: A:R.91 pi-Stacking: A:F.63 UDP.3: 11 residues within 4Å: Chain B: K.15, L.58, F.63, L.67, R.91, T.97, R.108, V.115, G.116, N.118 Ligands: MG.4 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:K.15, B:T.97, B:T.97, B:R.108, B:V.115, B:N.118, B:N.118 Water bridges: B:R.108, B:R.108 Salt bridges: B:R.91, B:R.108 pi-Stacking: B:F.63 UDP.5: 10 residues within 4Å: Chain C: K.15, L.58, F.63, L.67, R.91, T.97, V.115, G.116, N.118 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:K.15, C:T.97, C:R.108, C:V.115, C:N.118, C:N.118 Water bridges: C:R.91, C:R.91 Salt bridges: C:R.91, C:R.108 pi-Stacking: C:F.63 UDP.7: 11 residues within 4Å: Chain D: K.15, L.58, F.63, L.67, R.91, T.97, R.108, V.115, G.116, N.118 Ligands: MG.8 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:K.15, D:T.97, D:R.108, D:R.108, D:V.115, D:N.118, D:N.118 Water bridges: D:K.15, D:R.91, D:H.121 Salt bridges: D:R.91 pi-Stacking: D:F.63 UDP.9: 11 residues within 4Å: Chain E: K.15, L.58, F.63, L.67, R.91, T.97, R.108, V.115, G.116, N.118 Ligands: MG.10 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:V.115 Hydrogen bonds: E:K.15, E:R.108, E:V.115, E:N.118, E:N.118 Water bridges: E:K.15, E:H.121, E:H.121 Salt bridges: E:R.91, E:R.108 pi-Stacking: E:F.63 UDP.11: 11 residues within 4Å: Chain F: K.15, L.58, F.63, L.67, R.91, T.97, R.108, V.115, G.116, N.118 Ligands: MG.12 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:V.115 Hydrogen bonds: F:K.15, F:T.97, F:T.97, F:R.108, F:V.115, F:N.118, F:N.118 Water bridges: F:R.108, F:H.121 Salt bridges: F:R.91, F:R.108 pi-Stacking: F:F.63

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 2 residues within 4Å: Chain A: H.121 Ligands: UDP.1 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: UDP.3 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain C: H.121 Ligands: UDP.5 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain D: H.121 Ligands: UDP.7 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: UDP.9 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain F: R.91 Ligands: UDP.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Amjadi, R. et al., Mechanistic Insights into Substrate Recognition of Human Nucleoside Diphosphate Kinase C Based on Nucleotide-Induced Structural Changes. Int J Mol Sci (2024)

Release Date

2024-09-18

Peptides

Nucleoside diphosphate kinase 3: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Nucleoside diphosphate kinase 3

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