MolNFT v1 · #28341 · protein
Crystal structure analysis of uridylate kinase from neisseria meningitidis
1YBD: “Crystal structure analysis of uridylate kinase from neisseria meningitidis”. X-ray diffraction, 8 pockets (best druggability 0.56). MolNFT v1 #28341 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1YBD
- Type
- protein
- Length
- 708 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridylate kinase
- EC
- 2.7.4.-
- UniProt
- P65932
- Pockets
- 8 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Uridylate kinase (EC 2.7.4.-) | protein | 236 | 43% helix, 18% strand | P65932 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.56 | 0.78 | 43 | GOL |
| 2 | 133 | 0.55 | 0.82 | 20 | empty |
| 3 | 174 | 0.51 | 0.78 | 29 | empty |
| 4 | 171 | 0.50 | 0.78 | 28 | GOL |
| 5 | 109 | 0.44 | 0.78 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1586 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 497 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 modified (engineered).
Compared structures
- 1YBD · Crystal structure analysis of uridylate kinase from Neisseria meningitidis · the same entry in another collection · chain A against A, TM-score 1.00
- P65932 · AlphaFold monomer V2.0 prediction for uridylate kinase (P65932) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P65932
- Elsewhere: RCSB PDB 1YBD · PDBe 1YBD · UniProt P65932
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