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Structure and mutational analysis of a plant mitochondrial nucleoside diphosphate kinase: identification of residues involved in serine phosphorylation and oligomerization.
Analyse Structure and mutational analysis of a plant mitochondrial nucleoside… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1W7W
- Type
- protein
- Length
- 903 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside diphosphate kinase
- EC
- 2.7.4.6
- UniProt
- Q9SP13
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 151 | 46% helix, 16% strand | Q9SP13 |
| B, D, F | Nucleoside diphosphate kinase (EC 2.7.4.6) | protein | 150 | 44% helix, 16% strand | Q9SP13 |
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.86 | 0.87 | 112 | empty |
| 2 | 504 | 0.81 | 0.88 | 45 | empty |
| 3 | 237 | 0.52 | 0.76 | 31 | empty |
| 4 | 99 | 0.51 | 0.84 | 18 | empty |
| 5 | 231 | 0.51 | 0.75 | 31 | empty |
Interfaces
12 interfaces between chains.
- E–F · 1008 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1001 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1000 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 818 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 816 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1W7W · Structure and mutational analysis of a plant mitochondrial nucleoside diphosphate kinase… · the same entry in another collection · 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 Q9SP13
- Elsewhere: RCSB PDB 1W7W · PDBe 1W7W · UniProt Q9SP13
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