MolNFT v1 · #121728 · protein
Erwinia chrysanthemi L-asparaginase E63Q mutation + aspartic acid
5I3Z: “Erwinia chrysanthemi L-asparaginase E63Q mutation + aspartic acid”. X-ray diffraction, 1 ligand (ASP), 13 pockets (best druggability 0.84). MolNFT v1 #121728 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5I3Z
- Type
- protein
- Length
- 1,300 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
- ASP
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | L-asparaginase (EC 3.5.1.1) | protein | 325 | 32% helix, 24% strand | P06608 |
Ligands and binding sites
- ASP · Aspartic 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
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.84 | 0.92 | 51 | empty |
| 2 | 371 | 0.78 | 0.88 | 49 | ASP |
| 3 | 396 | 0.78 | 0.87 | 47 | ASP |
| 4 | 371 | 0.77 | 0.87 | 51 | ASP |
| 5 | 374 | 0.76 | 0.87 | 49 | ASP |
Interfaces
6 interfaces between chains.
- A–C · 2406 Ų buried · 44 hydrogen bonds · protein-protein
- B–D · 2386 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 1117 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1110 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1025 Ų buried · 16 hydrogen bonds · protein-protein
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 P06608
- Elsewhere: RCSB PDB 5I3Z · PDBe 5I3Z · UniProt P06608
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