SMTL ID : 8qvy.1

Human NDPK-C unliganded

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

homo-hexamer

Ligands

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 6 residues within 4Å: Chain A: K.15, Y.55, R.91, R.108, I.120, H.121 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.55, A:Y.55, A:R.91, A:R.108, A:I.120 Salt bridges: A:K.15, A:H.121 PO4.2: 4 residues within 4Å: Chain B: K.15, Y.55, R.91, H.121 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.55, B:R.91, B:R.108 Salt bridges: B:K.15, B:H.121 PO4.3: 4 residues within 4Å: Chain C: K.15, Y.55, R.91, H.121 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.91 Salt bridges: C:K.15, C:H.121 PO4.4: 6 residues within 4Å: Chain D: K.15, Y.55, R.91, R.108, H.121, G.122 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.55, D:R.108, D:G.122 Salt bridges: D:K.15, D:R.91, D:H.121 PO4.5: 5 residues within 4Å: Chain E: K.15, Y.55, R.91, N.118, H.121 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Y.55, E:N.118 Salt bridges: E:K.15, E:R.91, E:H.121 PO4.6: 6 residues within 4Å: Chain F: K.15, Y.55, R.108, N.118, H.121, G.122 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:R.108, F:N.118, F:I.120, F:G.122 Salt bridges: F:K.15, F:H.121

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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