Research workbench
Crystal structure of a 3-hydroxyproline dehydratse from agrobacterium vitis, target efi-506470, with bound pyrrole 2-carboxylate, ordered active site
Analyse Crystal structure of a 3-hydroxyproline dehydratse from agrobacterium vitis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K7G
- Type
- protein
- Length
- 690 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxyproline dehydratse
- UniProt
- B9K4G4
- Ligands
- PYC
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 3-hydroxyproline dehydratse | protein | 338 | 20% helix, 42% strand | B9K4G4 |
| D | 3-hydroxyproline dehydratse | protein | 352 | 19% helix, 41% strand | B9K4G4 |
Ligands and binding sites
- PYC · Pyrrole-2-carboxylate · ligand · 2 copies · chains B, D
- CIT · Citric acid · additive · 2 copies · chains B, D
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.82 | 0.98 | 33 | empty |
| 2 | 94 | 0.41 | 0.78 | 17 | empty |
| 3 | 91 | 0.38 | 0.76 | 16 | CIT |
| 4 | 89 | 0.37 | 0.76 | 16 | CIT |
| 5 | 89 | 0.35 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- B–D · 2307 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 4K7G · Crystal structure of a 3-hydroxyproline dehydratse from agrobacterium vitis, target… · the same entry in another collection · chain B against B, TM-score 1.00
- B9K4G4 · AlphaFold monomer V2.0 prediction for trans-3-hydroxy-L-proline dehydratase (B9K4G4) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 B9K4G4
- Elsewhere: RCSB PDB 4K7G · PDBe 4K7G · UniProt B9K4G4
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