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Crystal structure of the Asn-bound guinea pig L-asparaginase 1 catalytic domain active site mutant T19A
Analyse Crystal structure of the Asn-bound guinea pig L-asparaginase 1 catalytic domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DNC
- Type
- protein
- Length
- 1,419 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.01
- Source
- Cavia porcellus
- Molecule
- L-asparaginase
- UniProt
- H0W0T5
- Ligands
- ASN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.01 · 3 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | L-asparaginase | protein | 354 | 29% helix, 25% strand | H0W0T5 |
| B | L-asparaginase | protein | 355 | 28% helix, 25% strand | H0W0T5 |
| D | L-asparaginase | protein | 356 | 29% helix, 25% strand | H0W0T5 |
Ligands and binding sites
- ASN · Asparagine · ligand · 4 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.85 | 0.92 | 95 | EDO |
| 2 | 481 | 0.85 | 0.91 | 102 | EDO |
| 3 | 125 | 0.76 | 0.95 | 23 | empty |
| 4 | 134 | 0.76 | 0.94 | 19 | empty |
| 5 | 257 | 0.63 | 0.81 | 44 | ASN |
Interfaces
5 interfaces between chains.
- B–C · 2109 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 2076 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 1182 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1136 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5DNC · Crystal structure of the asn-bound guinea pig L-asparaginase 1 catalytic domain active… · the same entry in another collection · chain A 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 H0W0T5
- Elsewhere: RCSB PDB 5DNC · PDBe 5DNC · UniProt H0W0T5
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