Research workbench
Crystal structure of hydroxyproline dehydratase (hypd) from clostridioides difficile
Analyse Crystal structure of hydroxyproline dehydratase (hypd) from clostridioides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VXC
- Type
- protein
- Length
- 6,312 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trans-4-hydroxy-L-proline dehydratase
- EC
- 4.2.1.172
- UniProt
- A0A031WDE4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Trans-4-hydroxy-L-proline dehydratase (EC 4.2.1.172) | protein | 789 | 53% helix, 10% strand | A0A031WDE4 |
Ligands and binding sites
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 789 | 0.82 | 0.85 | 66 | empty |
| 2 | 749 | 0.82 | 0.85 | 66 | empty |
| 3 | 768 | 0.82 | 0.85 | 64 | empty |
| 4 | 781 | 0.81 | 0.84 | 61 | empty |
| 5 | 64 | 0.73 | 0.98 | 24 | empty |
Interfaces
12 interfaces between chains.
- E–F · 1363 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 1352 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1351 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1343 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 964 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6VXC · Crystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile · 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 A0A031WDE4
- Elsewhere: RCSB PDB 6VXC · PDBe 6VXC · UniProt A0A031WDE4
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