Research workbench
Crystal structure and allosteric regulation of the cytoplasmic escherichia COLI L-asparaginase I
Analyse Crystal structure and allosteric regulation of the cytoplasmic escherichia COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P2N
- Type
- protein
- Length
- 1,257 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase I
- EC
- 3.5.1.1
- UniProt
- P0A962
- Ligands
- ASN, ASP, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase I (EC 3.5.1.1) | protein | 306 | 31% helix, 24% strand | P0A962 |
| B | L-asparaginase I (EC 3.5.1.1) | protein | 321 | 31% helix, 23% strand | P0A962 |
| C | L-asparaginase I (EC 3.5.1.1) | protein | 309 | 30% helix, 24% strand | P0A962 |
| D | L-asparaginase I (EC 3.5.1.1) | protein | 321 | 31% helix, 23% strand | P0A962 |
Ligands and binding sites
- ASN · Asparagine · ligand · 5 copies · chains A, C, B, D
- ASP · Aspartic acid · ligand · chains B, D
- CL · Chloride ion · ion · 4 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.83 | 0.97 | 50 | ASN, EDO |
| 2 | 205 | 0.83 | 0.97 | 38 | ASN, EDO |
| 3 | 269 | 0.79 | 0.91 | 42 | empty |
| 4 | 918 | 0.74 | 0.78 | 93 | CL |
| 5 | 277 | 0.74 | 0.87 | 41 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1782 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1745 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1175 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1078 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 239 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2P2N · Crystal Structure and Allosteric Regulation of the Cytoplasmic Escherichia coli… · the same entry in another collection · chain D against D, TM-score 1.00
- P0A962 · AlphaFold monomer V2.0 prediction for L-asparaginase 1 (P0A962) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P0A962
- Elsewhere: RCSB PDB 2P2N · PDBe 2P2N · UniProt P0A962
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