Research workbench
L-asparaginase from escherichia COLI
Analyse L-asparaginase from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V5F
- Type
- protein
- Length
- 1,227 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
- 10 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase 2 (EC 3.5.1.1) | protein | 323 | 32% helix, 22% strand | P00805 |
| B | L-asparaginase 2 (EC 3.5.1.1) | protein | 300 | 33% helix, 23% strand | P00805 |
| C | L-asparaginase 2 (EC 3.5.1.1) | protein | 295 | 30% helix, 25% strand | P00805 |
| D | L-asparaginase 2 (EC 3.5.1.1) | protein | 309 | 33% helix, 23% strand | P00805 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 2 copies · chains A, C, B, D
- SIN · Succinic acid · additive · 2 copies · chains B, A, C
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 | 1011 | 0.87 | 0.88 | 134 | empty |
| 2 | 295 | 0.81 | 0.93 | 60 | empty |
| 3 | 201 | 0.64 | 0.84 | 33 | ASP |
| 4 | 65 | 0.60 | 0.91 | 26 | empty |
| 5 | 247 | 0.59 | 0.80 | 34 | SIN |
Interfaces
6 interfaces between chains.
- A–C · 2297 Ų buried · 48 hydrogen bonds · protein-protein
- B–D · 2212 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 1097 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1013 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 916 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
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 P00805
- Elsewhere: RCSB PDB 6V5F · PDBe 6V5F · UniProt P00805
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