MolNFT v1 · #21288 · protein

Structure of nucleoside diphosphate kinase 2 with bound dgtp from arabidopsis

1S59 · Nucleoside diphosphate kinase II: “Structure of nucleoside diphosphate kinase 2 with bound dgtp from arabidopsis”. X-ray diffraction, 2 ligands (DGI, DGT), 15 pockets (best druggability 0.83). MolNFT v1 #21288 on GenesisL1: 3D…

PDB: 1S59
Type: protein
Length: 906 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoside diphosphate kinase II
EC: 2.7.4.6
UniProt: O64903
Ligands: DGI, DGT
Pockets: 15 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, F	Nucleoside diphosphate kinase II (EC 2.7.4.6)	protein	153	43% helix, 18% strand	O64903
B, C, E	Nucleoside diphosphate kinase II (EC 2.7.4.6)	protein	149	46% helix, 16% strand	O64903

Ligands and binding sites

DGI · 2'-deoxyguanosine-5'-diphosphate · ligand · chains A, C
DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	371	0.83	0.92	56	empty
2	340	0.82	0.91	58	empty
3	392	0.82	0.90	54	empty
4	630	0.81	0.86	74	empty
5	259	0.55	0.77	33	DGT

Interfaces

12 interfaces between chains.

B–F · 1014 Å² buried · 17 hydrogen bonds · protein-protein
C–E · 999 Å² buried · 16 hydrogen bonds · protein-protein
A–D · 988 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 922 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 920 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

1S59 · Structure of nucleoside diphosphate kinase 2 with bound dGTP from Arabidopsis · the same entry in another collection · chain F against F, TM-score 1.00
O64903 · AlphaFold monomer V2.0 prediction for nucleoside diphosphate kinase II, chloroplastic… · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt O64903
Elsewhere: RCSB PDB 1S59 · PDBe 1S59 · UniProt O64903

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