Research workbench
Wolinella succinogenes L-asparaginase mutant V23Q,K24T with L-asp
Analyse Wolinella succinogenes L-asparaginase mutant V23Q,K24T with L-asp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RUE
- Type
- protein
- Length
- 1,264 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase
- EC
- 3.5.1.1
- UniProt
- P50286
- Ligands
- ASP
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase (EC 3.5.1.1) | protein | 318 | 34% helix, 21% strand | P50286 |
| B | L-asparaginase (EC 3.5.1.1) | protein | 314 | 34% helix, 24% strand | P50286 |
| C | L-asparaginase (EC 3.5.1.1) | protein | 315 | 34% helix, 22% strand | P50286 |
| D | L-asparaginase (EC 3.5.1.1) | protein | 317 | 34% helix, 24% strand | P50286 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 777 | 0.84 | 0.88 | 108 | empty |
| 2 | 66 | 0.70 | 0.97 | 34 | empty |
| 3 | 68 | 0.70 | 0.96 | 35 | empty |
| 4 | 99 | 0.67 | 0.91 | 22 | empty |
| 5 | 179 | 0.53 | 0.79 | 29 | ASP |
Interfaces
6 interfaces between chains.
- B–D · 2110 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 2077 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 945 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 935 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 868 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
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 P50286
- Elsewhere: RCSB PDB 6RUE · PDBe 6RUE · UniProt P50286
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