Research workbench
Crystal structure of ump kinase from ureaplasma parvum
Analyse Crystal structure of ump kinase from ureaplasma parvum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VA1
- Type
- protein
- Length
- 1,377 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate kinase
- EC
- 2.7.4.22, 2.7.4.-
- UniProt
- Q9PPX6
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uridylate kinase (EC 2.7.4.22, 2.7.4.-) | protein | 226 | 40% helix, 20% strand | Q9PPX6 |
| B | Uridylate kinase (EC 2.7.4.22, 2.7.4.-) | protein | 235 | 38% helix, 20% strand | Q9PPX6 |
| C | Uridylate kinase (EC 2.7.4.22, 2.7.4.-) | protein | 227 | 38% helix, 21% strand | Q9PPX6 |
| D | Uridylate kinase (EC 2.7.4.22, 2.7.4.-) | protein | 228 | 39% helix, 21% strand | Q9PPX6 |
| E | Uridylate kinase (EC 2.7.4.22, 2.7.4.-) | protein | 235 | 38% helix, 20% strand | Q9PPX6 |
| F | Uridylate kinase (EC 2.7.4.22, 2.7.4.-) | protein | 226 | 39% helix, 20% strand | Q9PPX6 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.78 | 0.80 | 68 | empty |
| 2 | 1174 | 0.78 | 0.80 | 83 | empty |
| 3 | 215 | 0.61 | 0.82 | 24 | empty |
| 4 | 266 | 0.60 | 0.79 | 36 | PO4 |
| 5 | 284 | 0.59 | 0.79 | 40 | PO4 |
Interfaces
12 interfaces between chains.
- E–F · 1643 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1594 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1555 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1108 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 1106 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
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 Q9PPX6
- Elsewhere: RCSB PDB 2VA1 · PDBe 2VA1 · UniProt Q9PPX6
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