Research workbench
Complex of double mutant (T89V,K162T) of E. COLI L-asparaginase II with L-asp
Analyse Complex of double mutant (T89V,K162T) of E. COLI L-asparaginase II 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
- 6V28
- Type
- protein
- Length
- 1,306 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
- Pockets
- 12 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-asparaginase 2 (EC 3.5.1.1) | protein | 326 | 34% helix, 24% strand | P00805 |
| C, D | L-asparaginase 2 (EC 3.5.1.1) | protein | 327 | 34% helix, 23% strand | P00805 |
Ligands and binding sites
- GOL · Glycerol · additive · 7 copies · chains B, C, D
- IMD · Imidazole · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.66 | 0.88 | 28 | empty |
| 2 | 142 | 0.64 | 0.86 | 29 | empty |
| 3 | 408 | 0.58 | 0.75 | 65 | empty |
| 4 | 108 | 0.48 | 0.80 | 23 | empty |
| 5 | 102 | 0.47 | 0.81 | 25 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2439 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 2432 Ų buried · 59 hydrogen bonds · protein-protein
- A–C · 253 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 modified (disulfide, nonstandard).
Compared structures
- 6V28 · Complex of double mutant (T89V,K162T) of E. coli L-asparaginase II with L-Asp · 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 6V28 · PDBe 6V28 · UniProt P00805
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