Research workbench
Crystal structure of a putative uridylate kinase (ump-kinase) from streptococcus pyogenes
Analyse Crystal structure of a putative uridylate kinase (ump-kinase) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z9D
- Type
- protein
- Length
- 714 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate kinase
- EC
- 2.7.4.-
- UniProt
- P65938
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Uridylate kinase (EC 2.7.4.-) | protein | 238 | 38% helix, 20% strand | P65938 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.75 | 0.78 | 76 | SO4 |
| 2 | 231 | 0.57 | 0.79 | 36 | SO4 |
| 3 | 246 | 0.57 | 0.79 | 33 | SO4 |
| 4 | 228 | 0.56 | 0.78 | 32 | SO4 |
| 5 | 51 | 0.46 | 0.85 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 212 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 210 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 206 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
- 1Z9D · Crystal structure of a putative uridylate kinase (UMP-kinase) from Streptococcus pyogenes · the same entry in another collection · chain A against A, TM-score 1.00
- P65938 · AlphaFold monomer V2.0 prediction for uridylate kinase (P65938) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P65938
- Elsewhere: RCSB PDB 1Z9D · PDBe 1Z9D · UniProt P65938
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