Research workbench
Crystal structure of the putative proline racemase from brucella melitensis, northeast structural genomics target LR31
Analyse Crystal structure of the putative proline racemase from brucella melitensis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TM0
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline racemase
- EC
- 5.1.1.4
- UniProt
- Q8YFD6
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Proline racemase (EC 5.1.1.4) | protein | 311 | 20% helix, 37% strand | Q8YFD6 |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.80 | 0.95 | 28 | empty |
| 2 | 358 | 0.56 | 0.75 | 56 | empty |
| 3 | 90 | 0.52 | 0.84 | 20 | empty |
| 4 | 230 | 0.51 | 0.76 | 34 | empty |
| 5 | 103 | 0.49 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 685 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 1TM0 · Crystal Structure of the putative proline racemase from Brucella melitensis, Northeast… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8YFD6 · AlphaFold monomer V2.0 prediction for protein BMEI1586 (Q8YFD6) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q8YFD6
- Elsewhere: RCSB PDB 1TM0 · PDBe 1TM0 · UniProt Q8YFD6
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