Research workbench
Complex of mutant (K162M) of E. COLI L-asparaginase II with L-asp. covalent acyl-enzyme intermediate.
Analyse Complex of mutant (K162M) of E. COLI L-asparaginase II with L-asp. covalent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V24
- Type
- protein
- Length
- 1,308 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase 2
- EC
- 3.5.1.1
- UniProt
- P00805
- Ligands
- ASP
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | L-asparaginase 2 (EC 3.5.1.1) | protein | 327 | 33% helix, 24% strand | P00805 |
| B, C | L-asparaginase 2 (EC 3.5.1.1) | protein | 327 | 33% helix, 24% strand | P00805 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.85 | 0.91 | 105 | empty |
| 2 | 238 | 0.80 | 0.93 | 63 | ASP |
| 3 | 242 | 0.79 | 0.92 | 61 | empty |
| 4 | 136 | 0.78 | 0.96 | 32 | empty |
| 5 | 178 | 0.69 | 0.88 | 32 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2438 Ų buried · 53 hydrogen bonds · protein-protein
- B–D · 2430 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 1102 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1081 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1051 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 6V24 · Complex of mutant (K162M) of E. coli L-asparaginase II with L-Asp. Covalent acyl-enzyme… · the same entry in another collection · chain D against D, TM-score 1.00
- P00805 · AlphaFold monomer V2.0 prediction for L-asparaginase 2 (P00805) · a predicted model of the same protein · chain C 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 P00805
- Elsewhere: RCSB PDB 6V24 · PDBe 6V24 · UniProt P00805
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.