Research workbench
X-ray structure of the complex between erwinia chrysanthemi L-asparaginase and L-glutamate
Analyse X-ray structure of the complex between erwinia chrysanthemi L-asparaginase and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HFW
- Type
- protein
- Length
- 1,229 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase
- EC
- 3.5.1.1
- UniProt
- P06608
- Ligands
- GLU
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase (EC 3.5.1.1) | protein | 307 | 33% helix, 22% strand | P06608 |
| B | L-asparaginase (EC 3.5.1.1) | protein | 309 | 33% helix, 22% strand | P06608 |
| C | L-asparaginase (EC 3.5.1.1) | protein | 307 | 33% helix, 22% strand | P06608 |
| D | L-asparaginase (EC 3.5.1.1) | protein | 306 | 33% helix, 25% strand | P06608 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.82 | 0.92 | 47 | empty |
| 2 | 172 | 0.79 | 0.95 | 47 | empty |
| 3 | 164 | 0.78 | 0.95 | 45 | empty |
| 4 | 428 | 0.62 | 0.77 | 47 | GLU |
| 5 | 392 | 0.61 | 0.77 | 38 | GLU |
Interfaces
6 interfaces between chains.
- A–C · 2261 Ų buried · 44 hydrogen bonds · protein-protein
- B–D · 2249 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 1147 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1125 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 838 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1HFW · X-ray structure of the complex between Erwinia chrysanthemi L-asparaginase and L-Glutamate · the same entry in another collection · chain A against A, TM-score 1.00
- P06608 · AlphaFold monomer V2.0 prediction for L-asparaginase (P06608) · 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 P06608
- Elsewhere: RCSB PDB 1HFW · PDBe 1HFW · UniProt P06608
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