SMTL ID : 8qw3.1

Human NDPK-C in complex with ADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 11 residues within 4Å: Chain A: K.15, Y.55, L.58, F.63, L.67, R.91, T.97, R.108, V.115, N.118 Chain B: E.155 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:K.15, A:R.108, A:N.118, A:N.118 Water bridges: A:K.15, A:R.91, A:R.91, A:T.97, A:T.97, A:T.97, A:R.108, A:I.120, A:H.121, A:G.122 Salt bridges: A:R.91, A:R.108 pi-Stacking: A:F.63, A:F.63 ADP.2: 10 residues within 4Å: Chain B: K.15, Y.55, L.58, F.63, L.67, T.97, R.108, V.115, N.118 Chain C: E.155 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:K.15, B:R.108, B:N.118, B:N.118 Water bridges: B:K.15, B:R.91, B:T.97, B:T.97, B:R.108, B:I.120, B:H.121 Salt bridges: B:R.108 pi-Stacking: B:F.63, B:F.63 ADP.4: 11 residues within 4Å: Chain A: E.155 Chain C: K.15, Y.55, L.58, F.63, L.67, R.91, T.97, R.108, V.115, N.118 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:K.15, C:N.118, C:N.118 Water bridges: C:K.15, C:G.95, C:R.108, C:R.108, C:I.120 Salt bridges: C:R.91, C:R.108 pi-Stacking: C:F.63, C:F.63 ADP.6: 8 residues within 4Å: Chain D: K.15, L.58, F.63, L.67, T.97, R.108, V.115, N.118 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:K.15, D:R.108, D:N.118, D:N.118 Water bridges: D:R.91, D:T.97, D:T.97, D:R.108, D:I.120 Salt bridges: D:R.108 pi-Stacking: D:F.63, D:F.63 ADP.7: 10 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 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:K.15, E:N.118, E:N.118 Water bridges: E:K.15, E:R.91, E:R.91, E:R.108, E:R.108 Salt bridges: E:R.91, E:R.108 pi-Stacking: E:F.63, E:F.63 ADP.9: 10 residues within 4Å: Chain E: E.155 Chain F: K.15, Y.55, L.58, F.63, L.67, T.97, R.108, V.115, N.118 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:K.15, F:R.108, F:N.118, F:N.118 Water bridges: F:K.15, F:T.97, F:R.108, F:R.108, F:I.120, F:H.121, F:D.124, F:D.124 Salt bridges: F:R.108 pi-Stacking: F:F.63, F:F.63

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain B: G.5, A.6, H.7, E.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.6, B:H.7, B:E.8 Salt bridges: B:H.7 SO4.5: 8 residues within 4Å: Chain C: G.1, H.2, M.3, T.4, G.5, A.6, H.7, E.8 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:G.1, C:G.1, C:T.4, C:G.5, C:A.6, C:H.7, C:E.8 Salt bridges: C:H.7 SO4.8: 8 residues within 4Å: Chain E: G.1, H.2, M.3, T.4, G.5, A.6, H.7, E.8 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:G.1, E:G.1, E:M.3, E:T.4, E:G.5, E:A.6, E:H.7, E:E.8 Salt bridges: E:H.7

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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