MolNFT v1 · #56290 · protein
Crystal structure of E. COLI isoaspartyl AMINOPEPTIDASE/L-asparaginase in complex with L-aspartate
2ZAL: “Crystal structure of E. COLI isoaspartyl AMINOPEPTIDASE/L-asparaginase in complex with L-aspartate”. X-ray diffraction, 4 ligands (ASP, CA, NA), 5 pockets (best druggability 0.58). MolNFT v1 #56290 on GenesisL1: 3D structure…
- PDB
- 2ZAL
- Type
- protein
- Length
- 586 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase
- EC
- 3.4.19.5, 3.5.1.1
- UniProt
- P37595
- Ligands
- ASP, CA, NA, CL
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase (EC 3.4.19.5, 3.5.1.1) | protein | 160 | 49% helix, 16% strand | P37595 |
| B, D | L-asparaginase (EC 3.4.19.5, 3.5.1.1) | protein | 135 | 23% helix, 36% strand | P37595 |
| C | L-asparaginase (EC 3.4.19.5, 3.5.1.1) | protein | 156 | 46% helix, 16% strand | P37595 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 5 copies · chains A, B, C, D
- CA · Calcium ion · metal · 5 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · chains C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.58 | 0.80 | 40 | ASP |
| 2 | 313 | 0.58 | 0.77 | 32 | ASP |
| 3 | 276 | 0.52 | 0.75 | 43 | empty |
| 4 | 61 | 0.38 | 0.79 | 15 | empty |
| 5 | 58 | 0.36 | 0.79 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2884 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 2862 Ų buried · 57 hydrogen bonds · protein-protein
- B–D · 570 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 526 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 511 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2ZAL · Crystal structure of E. coli isoaspartyl aminopeptidase/L-asparaginase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P37595 · AlphaFold monomer V2.0 prediction for isoaspartyl peptidase (P37595) · a predicted model of the same protein · chain D 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 P37595
- Elsewhere: RCSB PDB 2ZAL · PDBe 2ZAL · UniProt P37595
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