SMTL ID : 8qw0.1 (1 other biounit)

Human NDPK-C in complex with GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-hexamer

Ligands

6 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 9 residues within 4Å: Chain A: K.15, L.58, F.63, L.67, R.91, T.97, R.108, V.115, N.118 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.15, A:R.108, A:N.118, A:N.118 Water bridges: A:K.15, A:G.116, B:E.155 Salt bridges: A:R.91, A:R.108 pi-Stacking: A:F.63, A:F.63 GDP.2: 13 residues within 4Å: Chain B: K.15, E.57, L.58, F.63, R.66, L.67, R.91, T.97, R.108, V.115, G.116, N.118 Chain C: E.155 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.15, B:E.57, B:R.66, B:T.97, B:R.108, B:N.118, B:N.118, C:E.155 Water bridges: B:R.91, B:I.120 Salt bridges: B:R.91, B:R.108 pi-Stacking: B:F.63, B:F.63 pi-Cation interactions: B:F.63 GDP.3: 12 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, G.116, N.118 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:K.15, C:R.108, C:N.118, C:N.118, C:H.121, A:E.155 Salt bridges: C:R.91, C:R.108 pi-Stacking: C:F.63, C:F.63 GDP.5: 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: SO4.6 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:K.15, D:R.66, D:R.108, D:N.118, D:N.118 Water bridges: D:H.121, F:E.155 Salt bridges: D:R.91, D:R.108 pi-Stacking: D:F.63, D:F.63 GDP.7: 11 residues within 4Å: Chain D: E.155 Chain E: K.15, Y.55, L.58, F.63, L.67, R.91, T.97, R.108, V.115, N.118 13 PLIP interactions: 2 interactions with chain D, 11 interactions with chain E Hydrogen bonds: D:E.155, D:E.155, E:K.15, E:T.97, E:T.97, E:R.108, E:N.118, E:N.118 Water bridges: E:H.121 Salt bridges: E:R.91, E:R.108 pi-Stacking: E:F.63, E:F.63 GDP.8: 13 residues within 4Å: Chain E: E.155 Chain F: K.15, Y.55, L.58, F.63, L.67, R.91, T.97, R.108, V.115, G.116, N.118, H.121 12 PLIP interactions: 11 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:K.15, F:T.97, F:T.97, F:R.108, F:N.118, F:N.118, E:E.155 Water bridges: F:K.15 Salt bridges: F:R.91, F:R.108 pi-Stacking: F:F.63, F:F.63

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

SO4.4: 3 residues within 4Å: Chain C: G.5, A.6, H.7 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.6, C:H.7 Salt bridges: C:H.7 SO4.6: 2 residues within 4Å: Chain D: R.66 Ligands: GDP.5 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.66

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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