MolNFT v1 · #47564 · protein
Crystal structure and allosteric regulation of the cytoplasmic escherichia COLI L-asparaginase I
2P2D: “Crystal structure and allosteric regulation of the cytoplasmic escherichia COLI L-asparaginase I”. X-ray diffraction, 17 pockets (best druggability 0.84). MolNFT v1 #47564 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2P2D
- Type
- protein
- Length
- 1,321 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
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase I (EC 3.5.1.1) | protein | 330 | 32% helix, 25% strand | P0A962 |
| B | L-asparaginase I (EC 3.5.1.1) | protein | 329 | 33% helix, 21% strand | P0A962 |
| C | L-asparaginase I (EC 3.5.1.1) | protein | 331 | 32% helix, 22% strand | P0A962 |
| D | L-asparaginase I (EC 3.5.1.1) | protein | 331 | 31% helix, 22% strand | P0A962 |
Ligands and binding sites
- GOL · Glycerol · additive · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.84 | 0.95 | 50 | GOL |
| 2 | 254 | 0.82 | 0.94 | 41 | GOL |
| 3 | 750 | 0.76 | 0.81 | 66 | empty |
| 4 | 723 | 0.76 | 0.81 | 64 | empty |
| 5 | 103 | 0.56 | 0.85 | 26 | GOL |
Interfaces
4 interfaces between chains.
- B–D · 2167 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 2161 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 963 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 941 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2P2D · 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 B 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 2P2D · PDBe 2P2D · UniProt P0A962
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