Research workbench
Crystal structure of hydroxyproline dehydratase (hypd) from clostridioides difficile with substrate trans-4-hydroxy-L-proline bound
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
- 6VXE
- 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
- Ligands
- HYP
- Pockets
- 20 · best druggability 0.83
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
- HYP · 4-hydroxyproline · ligand · 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 | 694 | 0.83 | 0.87 | 66 | empty |
| 2 | 689 | 0.82 | 0.86 | 63 | empty |
| 3 | 727 | 0.82 | 0.85 | 62 | empty |
| 4 | 716 | 0.81 | 0.84 | 61 | empty |
| 5 | 633 | 0.64 | 0.74 | 58 | empty |
Interfaces
11 interfaces between chains.
- G–H · 1401 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1392 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1384 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1384 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 956 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6VXE · Crystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile with… · 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 6VXE · PDBe 6VXE · UniProt A0A031WDE4
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