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Structure of the isoaspartyl peptidase with L-asparaginase activity from E. COLI
Analyse Structure of the isoaspartyl peptidase with L-asparaginase activity from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T3M
- Type
- protein
- Length
- 580 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative L-asparaginase
- EC
- 3.5.1.1
- UniProt
- P37595
- Ligands
- NA, NO3
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative L-asparaginase (EC 3.5.1.1) | protein | 156 | 48% helix, 17% strand | P37595 |
| B, D | Putative L-asparaginase (EC 3.5.1.1) | protein | 134 | 23% helix, 37% strand | P37595 |
| C | Putative L-asparaginase (EC 3.5.1.1) | protein | 156 | 48% helix, 17% strand | P37595 |
Ligands and binding sites
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 | 261 | 0.60 | 0.79 | 39 | empty |
| 2 | 280 | 0.58 | 0.78 | 39 | NO3 |
| 3 | 254 | 0.54 | 0.77 | 33 | empty |
| 4 | 64 | 0.43 | 0.82 | 17 | empty |
| 5 | 61 | 0.39 | 0.80 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2856 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 2798 Ų buried · 51 hydrogen bonds · protein-protein
- B–D · 565 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 502 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 490 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1T3M · Structure of the isoaspartyl peptidase with L-asparaginase activity from E. coli · 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 B 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 1T3M · PDBe 1T3M · UniProt P37595
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