Research workbench
Structure of putative asparaginase encoded by escherichia COLI ybik gene
Analyse Structure of putative asparaginase encoded by escherichia COLI ybik gene in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JN9
- Type
- protein
- Length
- 584 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
- CA, NA, CL
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative L-asparaginase (EC 3.5.1.1) | protein | 158 | 47% helix, 18% strand | P37595 |
| B | 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 | 157 | 46% helix, 18% strand | P37595 |
| D | Putative L-asparaginase (EC 3.5.1.1) | protein | 135 | 23% helix, 36% strand | P37595 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · 4 copies · chains A, C, D, B
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 | 392 | 0.61 | 0.77 | 42 | empty |
| 2 | 290 | 0.58 | 0.78 | 36 | empty |
| 3 | 266 | 0.52 | 0.75 | 38 | empty |
| 4 | 57 | 0.38 | 0.80 | 18 | empty |
| 5 | 53 | 0.25 | 0.72 | 12 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2842 Ų buried · 61 hydrogen bonds · protein-protein
- C–D · 2841 Ų buried · 55 hydrogen bonds · protein-protein
- B–D · 563 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 524 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 491 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 1JN9 · Structure of Putative Asparaginase Encoded by Escherichia coli ybiK Gene · the same entry in another collection · chain D against D, 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 1JN9 · PDBe 1JN9 · UniProt P37595
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