MolNFT v1 · #104168 · protein
Crystal structure of probable proline racemase from agrobacterium radiobacter K84, target efi-506561, with bound carbonate
4Q2H · Proline racemase protein: “Crystal structure of probable proline racemase from agrobacterium radiobacter K84, target efi-506561, with…”. X-ray diffraction, 1 ligand (BCT), 9 pockets (best druggability 0.84). MolNFT v1 #104168 on…
- PDB
- 4Q2H
- Type
- protein
- Length
- 686 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline racemase protein
- UniProt
- B9J8G8
- Ligands
- BCT
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline racemase protein | protein | 346 | 23% helix, 41% strand | B9J8G8 |
| B | Proline racemase protein | protein | 340 | 22% helix, 41% strand | B9J8G8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.84 | 0.97 | 43 | empty |
| 2 | 83 | 0.41 | 0.78 | 16 | empty |
| 3 | 72 | 0.38 | 0.79 | 23 | empty |
| 4 | 100 | 0.38 | 0.76 | 20 | empty |
| 5 | 83 | 0.36 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1793 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 4Q2H · Crystal structure of probable proline racemase from agrobacterium radiobacter K84, TARGET… · the same entry in another collection · chain A against A, TM-score 1.00
- B9J8G8 · AlphaFold monomer V2.0 prediction for 4-hydroxyproline 2-epimerase 1 (B9J8G8) · 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 B9J8G8
- Elsewhere: RCSB PDB 4Q2H · PDBe 4Q2H · UniProt B9J8G8
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