Research workbench
L-asparaginase from erwinia carotovora in complex with aspartic acid
Analyse L-asparaginase from erwinia carotovora in complex with aspartic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GVN
- Type
- protein
- Length
- 2,600 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase
- EC
- 3.5.1.1
- Ligands
- ASP
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | L-asparaginase (EC 3.5.1.1) | protein | 325 | 31% helix, 20% strand | — |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 8 copies · chains A, E, B, F, C, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.89 | 0.92 | 134 | empty |
| 2 | 933 | 0.89 | 0.92 | 128 | empty |
| 3 | 1095 | 0.79 | 0.81 | 98 | ASP |
| 4 | 362 | 0.74 | 0.86 | 59 | ASP |
| 5 | 381 | 0.74 | 0.85 | 57 | ASP |
Interfaces
15 interfaces between chains.
- C–G · 2323 Ų buried · 47 hydrogen bonds · protein-protein
- B–F · 2321 Ų buried · 46 hydrogen bonds · protein-protein
- D–H · 2312 Ų buried · 45 hydrogen bonds · protein-protein
- A–E · 2300 Ų buried · 47 hydrogen bonds · protein-protein
- D–G · 1142 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 2GVN · L-asparaginase from Erwinia carotovora in complex with aspartic acid · the same entry in another collection · chain H against H, 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
- Elsewhere: RCSB PDB 2GVN · PDBe 2GVN
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.