MolNFT v1 · #114073 · protein
Picrophilus torridus aspartate racemase
5B19: “Picrophilus torridus aspartate racemase”. X-ray diffraction, 3 pockets (best druggability 0.54). MolNFT v1 #114073 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5B19
- Type
- protein
- Length
- 378 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate racemase
- EC
- 5.1.1.13
- UniProt
- Q6L2R8
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate racemase (EC 5.1.1.13) | protein | 231 | 52% helix, 14% strand | Q6L2R8 |
| B | Aspartate racemase (EC 5.1.1.13) | protein | 147 | 50% helix, 12% strand | Q6L2R8 |
Ligands and binding sites
- TLA · L(+)-tartaric acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.54 | 0.86 | 21 | TLA |
| 2 | 79 | 0.35 | 0.76 | 16 | empty |
| 3 | 53 | 0.32 | 0.77 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1426 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5B19 · Picrophilus torridus aspartate racemase · the same entry in another collection · chain A against A, TM-score 1.00
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 Q6L2R8
- Elsewhere: RCSB PDB 5B19 · PDBe 5B19 · UniProt Q6L2R8
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