Research workbench
Crystal structure of hydantoin racemase from pyrococcus horikoshii OT3
Analyse Crystal structure of hydantoin racemase from pyrococcus horikoshii OT3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EQ5
- Type
- protein
- Length
- 844 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 228AA long hypothetical hydantoin racemase
- EC
- 5.1.-.-
- UniProt
- O58781
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 228AA long hypothetical hydantoin racemase (EC 5.1.-.-) | protein | 215 | 50% helix, 17% strand | O58781 |
| B | 228AA long hypothetical hydantoin racemase (EC 5.1.-.-) | protein | 214 | 47% helix, 17% strand | O58781 |
| D | 228AA long hypothetical hydantoin racemase (EC 5.1.-.-) | protein | 200 | 45% helix, 19% strand | O58781 |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.72 | 0.77 | 92 | empty |
| 2 | 465 | 0.68 | 0.80 | 53 | empty |
| 3 | 383 | 0.64 | 0.78 | 48 | empty |
| 4 | 231 | 0.51 | 0.76 | 29 | empty |
| 5 | 193 | 0.50 | 0.76 | 24 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1536 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1460 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 730 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2EQ5 · Crystal structure of hydantoin racemase from Pyrococcus horikoshii OT3 · 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 O58781
- Elsewhere: RCSB PDB 2EQ5 · PDBe 2EQ5 · UniProt O58781
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