SMTL ID : 8qw1.1

Human NDPK-C in complex with ADP and Mg2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 11 residues within 4Å: Chain A: K.15, L.58, R.61, F.63, L.67, R.91, T.97, V.115, N.118 Chain B: E.155 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.15, A:N.118, A:N.118 Water bridges: A:R.91, A:R.108, A:R.108, A:I.120, A:H.121, A:H.121, A:D.124 Salt bridges: A:R.61, A:R.91 pi-Stacking: A:F.63, A:F.63 ADP.3: 10 residues within 4Å: Chain B: K.15, L.58, F.63, L.67, R.91, T.97, V.115, N.118 Chain C: E.155 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.15, B:T.97, B:N.118, B:N.118 Water bridges: B:R.91, B:R.108, B:R.108, B:I.120 Salt bridges: B:R.91 pi-Stacking: B:F.63, B:F.63 ADP.5: 12 residues within 4Å: Chain A: E.155 Chain C: K.15, L.58, R.61, F.63, L.67, R.91, T.97, V.115, G.116, N.118 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:K.15, C:R.61, C:T.97, C:R.108, C:N.118, C:N.118 Water bridges: C:R.91, C:R.108, C:I.120, C:G.122 Salt bridges: C:R.91 pi-Stacking: C:F.63, C:F.63 ADP.7: 11 residues within 4Å: Chain D: K.15, L.58, F.63, R.66, L.67, R.91, T.97, R.108, V.115, N.118 Ligands: MG.8 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:K.15, D:R.66, D:N.118, D:N.118 Water bridges: D:R.91, D:R.108, D:R.108, D:R.108 Salt bridges: D:R.91, D:R.108 pi-Stacking: D:F.63 ADP.9: 11 residues within 4Å: Chain D: E.155 Chain E: K.15, L.58, F.63, L.67, R.91, T.97, R.108, V.115, N.118 Ligands: MG.10 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:K.15, E:N.118, E:N.118 Water bridges: E:R.91, E:R.108, E:R.108, E:I.120, E:H.121, E:H.121 Salt bridges: E:R.91, E:R.108 pi-Stacking: E:F.63, E:F.63 ADP.11: 13 residues within 4Å: Chain E: E.155 Chain F: K.15, L.58, F.63, R.66, 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 Hydrogen bonds: F:K.15, F:R.66, F:T.97, F:R.108, F:R.108, F:N.118, F:N.118 Water bridges: F:I.120, F:H.121, F:H.121, F:G.122 Salt bridges: F:R.91 pi-Stacking: F:F.63

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

MG.2: 1 residues within 4Å: Ligands: ADP.1 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: ADP.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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