MolNFT v1 · #96212 · protein
Crystal structure of PPUT_1285, a putative hydroxyproline epimerase from pseudomonas putida F1 (target efi-506500), open form, space group P212121, bound sulfate
4JD7 · Proline racemase: “Crystal structure of PPUT_1285, a putative hydroxyproline epimerase from pseudomonas putida F1 (target…”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.71). MolNFT v1 #96212 on GenesisL1: 3D…
- PDB
- 4JD7
- Type
- protein
- Length
- 626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline racemase
- UniProt
- A5VZY6
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline racemase | protein | 314 | 22% helix, 40% strand | A5VZY6 |
| D | Proline racemase | protein | 312 | 24% helix, 41% strand | A5VZY6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.71 | 0.85 | 42 | SO4 |
| 2 | 342 | 0.66 | 0.80 | 38 | SO4 |
| 3 | 265 | 0.53 | 0.75 | 30 | empty |
| 4 | 112 | 0.38 | 0.75 | 23 | empty |
| 5 | 63 | 0.33 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–D · 156 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4JD7 · Crystal structure of pput_1285, a putative hydroxyproline epimerase from Pseudomonas… · the same entry in another collection · chain A against A, TM-score 1.00
- A5VZY6 · AlphaFold monomer V2.0 prediction for 4-hydroxyproline 2-epimerase (A5VZY6) · a predicted model of the same protein · chain D against A, TM-score 0.91
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 A5VZY6
- Elsewhere: RCSB PDB 4JD7 · PDBe 4JD7 · UniProt A5VZY6
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