MolNFT v1 · #21286 · protein
Crystal structure of nucleoside diphosphate kinase 2 from arabidopsis
1S57 · Nucleoside diphosphate kinase II: “Crystal structure of nucleoside diphosphate kinase 2 from arabidopsis”. X-ray diffraction, 1 ligand (SO4), 15 pockets (best druggability 0.83). MolNFT v1 #21286 on GenesisL1: 3D structure, binding…
- PDB
- 1S57
- 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
- SO4
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F | Nucleoside diphosphate kinase II (EC 2.7.4.6) | protein | 153 | 41% helix, 18% strand | O64903 |
| B, C, E | Nucleoside diphosphate kinase II (EC 2.7.4.6) | protein | 149 | 44% helix, 17% strand | O64903 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, D, E, F
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 6 copies · chains A, D, B, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.83 | 0.91 | 55 | EPE |
| 2 | 365 | 0.82 | 0.91 | 53 | EPE |
| 3 | 385 | 0.81 | 0.90 | 50 | EPE |
| 4 | 541 | 0.80 | 0.86 | 72 | empty |
| 5 | 221 | 0.52 | 0.76 | 28 | SO4 |
Interfaces
12 interfaces between chains.
- B–F · 1036 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 995 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 989 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 910 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 903 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1S57 · crystal structure of nucleoside diphosphate kinase 2 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 1S57 · PDBe 1S57 · UniProt O64903
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