Research workbench
Crystal structure of putative asparaginase encoded by escherichia COLI ybik gene
Analyse Crystal 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
- 1K2X
- Type
- protein
- Length
- 582 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, CL
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative L-asparaginase (EC 3.5.1.1) | protein | 156 | 47% helix, 17% strand | P37595 |
| B, D | Putative L-asparaginase (EC 3.5.1.1) | protein | 135 | 23% helix, 37% strand | P37595 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.55 | 0.79 | 36 | empty |
| 2 | 237 | 0.54 | 0.77 | 29 | empty |
| 3 | 229 | 0.50 | 0.75 | 36 | empty |
| 4 | 52 | 0.42 | 0.83 | 17 | empty |
| 5 | 50 | 0.38 | 0.81 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2823 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 2810 Ų buried · 55 hydrogen bonds · protein-protein
- B–D · 580 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 515 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 509 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 1K2X · Crystal structure of putative asparaginase encoded by Escherichia coli ybiK gene · the same entry in another collection · chain C against C, 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 0.99
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 1K2X · PDBe 1K2X · UniProt P37595
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