MolNFT v1 · #162378 · protein
Crystal structure of trans-3-hydroxy-L-proline dehydratase from thermococcus litoralis - open conformation
6R76 · Proline racemase: “Crystal structure of trans-3-hydroxy-L-proline dehydratase from thermococcus litoralis - open conformation”. X-ray diffraction, 19 pockets (best druggability 0.80). MolNFT v1 #162378 on GenesisL1: 3D structure…
- PDB
- 6R76
- Type
- protein
- Length
- 1,369 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline racemase
- UniProt
- H3ZMH8
- Pockets
- 19 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline racemase | protein | 348 | 22% helix, 39% strand | H3ZMH8 |
| B | Proline racemase | protein | 336 | 22% helix, 41% strand | H3ZMH8 |
| C | Proline racemase | protein | 345 | 23% helix, 40% strand | H3ZMH8 |
| D | Proline racemase | protein | 340 | 22% helix, 41% strand | H3ZMH8 |
Pockets
19 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.80 | 0.82 | 89 | empty |
| 2 | 400 | 0.75 | 0.85 | 40 | empty |
| 3 | 394 | 0.69 | 0.81 | 51 | empty |
| 4 | 84 | 0.53 | 0.84 | 16 | empty |
| 5 | 84 | 0.50 | 0.83 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2752 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2734 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 66 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6R76 · Crystal structure of trans-3-Hydroxy-L-proline dehydratase from Thermococcus litoralis… · 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 H3ZMH8
- Elsewhere: RCSB PDB 6R76 · PDBe 6R76 · UniProt H3ZMH8
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