Research workbench
Crystal structure of a 4-hydroxyproline epimerase from burkholderia multivorans atcc 17616, target efi-506586, open form, with bound pyrrole-2-carboxylate
Analyse Crystal structure of a 4-hydroxyproline epimerase from burkholderia multivorans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q60
- Type
- protein
- Length
- 621 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline racemase
- EC
- 5.1.1.4
- UniProt
- B3D6W2
- Ligands
- PYC
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline racemase (EC 5.1.1.4) | protein | 311 | 22% helix, 38% strand | B3D6W2 |
| B | Proline racemase (EC 5.1.1.4) | protein | 310 | 22% helix, 39% strand | B3D6W2 |
Ligands and binding sites
- PYC · Pyrrole-2-carboxylate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 918 | 0.78 | 0.81 | 97 | GOL |
| 2 | 230 | 0.69 | 0.85 | 34 | PYC |
| 3 | 202 | 0.68 | 0.86 | 31 | PYC |
| 4 | 79 | 0.40 | 0.79 | 16 | empty |
| 5 | 50 | 0.36 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1228 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4Q60 · Crystal structure of a 4-hydroxyproline epimerase from Burkholderia Multivorans atcc… · the same entry in another collection · chain A against A, TM-score 1.00
- B3D6W2 · AlphaFold monomer V2.0 prediction for 4-hydroxyproline 2-epimerase 1 (B3D6W2) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 B3D6W2
- Elsewhere: RCSB PDB 4Q60 · PDBe 4Q60 · UniProt B3D6W2
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