SMTL ID : 8qw0.2 (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: 11 residues within 4Å: Chain A: K.15, Y.55, L.58, F.63, R.66, L.67, R.91, T.97, R.108, V.115, N.118 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.15, A:R.66, A:R.91, A:T.97, A:R.108, A:N.118, A:N.118, B:E.155 Water bridges: A:K.15, A:G.122 Salt bridges: A:R.108 pi-Stacking: A:F.63, A:F.63 GDP.2: 11 residues within 4Å: Chain B: K.15, Y.55, L.58, F.63, L.67, T.97, R.108, V.115, G.116, N.118 Chain C: E.155 13 PLIP interactions: 1 interactions with chain C, 12 interactions with chain B Hydrogen bonds: C:E.155, B:K.15, B:R.108, B:N.118, B:N.118, B:H.121 Water bridges: B:K.15, B:R.108, B:I.120 Salt bridges: 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, N.118, H.121 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:K.15, C:R.108, C:N.118, C:N.118, A:E.155, A:E.155 Salt bridges: C:K.15, C:R.91, C:R.108, C:H.121 pi-Stacking: C:F.63, C:F.63 GDP.4: 10 residues within 4Å: Chain D: K.15, L.58, F.63, L.67, T.97, R.108, V.115, N.118, H.121, G.122 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:K.15, D:T.97, D:R.108, D:N.118, D:N.118, D:G.122 Water bridges: D:R.108, D:G.122, F:E.155 Salt bridges: D:R.108, D:H.121 pi-Stacking: D:F.63, D:F.63 GDP.5: 12 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, G.116, N.118, G.122 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:K.15, E:T.97, E:N.118, E:N.118, E:G.122, D:E.155 Salt bridges: E:R.91, E:R.108 pi-Stacking: E:F.63, E:F.63 GDP.6: 10 residues within 4Å: Chain E: E.155 Chain F: 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 F, 1 interactions with chain E Hydrogen bonds: F:K.15, F:R.108, F:N.118, F:N.118, E:E.155 Water bridges: F:H.121 Salt bridges: F:R.91, F:R.108 pi-Stacking: F:F.63, F:F.63 pi-Cation interactions: F:F.63

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
G

B
H

C
I

D
J

E
K

F
L

Nucleoside diphosphate kinase 3

Related Entries With Identical Sequence