Research workbench
Complex of double mutant (T89V,K162T) of E. COLI L-asparaginase II with L-asn
Analyse Complex of double mutant (T89V,K162T) of E. COLI L-asparaginase II with L-asn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V2B
- Type
- protein
- Length
- 1,290 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
- ASN
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | L-asparaginase 2 (EC 3.5.1.1) | protein | 326 | 33% helix, 23% strand | P00805 |
| B | L-asparaginase 2 (EC 3.5.1.1) | protein | 312 | 34% helix, 24% strand | P00805 |
Ligands and binding sites
- ASN · Asparagine · ligand · 4 copies · chains A, B, C, D
- CIT · Citric acid · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.72 | 0.96 | 24 | empty |
| 2 | 129 | 0.65 | 0.88 | 28 | empty |
| 3 | 168 | 0.61 | 0.84 | 32 | ASN |
| 4 | 367 | 0.58 | 0.76 | 50 | empty |
| 5 | 127 | 0.55 | 0.83 | 33 | ASN |
Interfaces
3 interfaces between chains.
- C–D · 2404 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 2307 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 280 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6V2B · Complex of double mutant (T89V,K162T) of E. coli L-asparaginase II with L-Asn · 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 6V2B · PDBe 6V2B · UniProt P00805
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.