Research workbench
Crystal structure of uncharacterized conserved protein from geobacillus kaustophilus
Analyse Crystal structure of uncharacterized conserved protein from geobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YYT
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orotidine 5'-phosphate decarboxylase
- EC
- 4.1.1.23
- UniProt
- Q5L0U0
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) | protein | 215 | 53% helix, 18% strand | Q5L0U0 |
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.71 | 0.98 | 25 | empty |
| 2 | 53 | 0.71 | 0.98 | 26 | empty |
| 3 | 277 | 0.59 | 0.79 | 49 | empty |
| 4 | 250 | 0.59 | 0.79 | 39 | empty |
| 5 | 459 | 0.59 | 0.75 | 59 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1906 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1862 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 349 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 137 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2YYT · Crystal structure of uncharacterized conserved protein from Geobacillus kaustophilus · the same entry in another collection · chain A against A, TM-score 1.00
- Q5L0U0 · AlphaFold monomer V2.0 prediction for orotidine 5'-phosphate decarboxylase (Q5L0U0) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q5L0U0
- Elsewhere: RCSB PDB 2YYT · PDBe 2YYT · UniProt Q5L0U0
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