MolNFT v1 · #147814 · protein
Crystal structure of E. COLI L-asparaginase II
6EOK · L-asparaginase 2: “Crystal structure of E. COLI L-asparaginase II”. X-ray diffraction, 1 ligand (ZN), 12 pockets (best druggability 0.87). MolNFT v1 #147814 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6EOK
- Type
- protein
- Length
- 1,212 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase 2
- EC
- 3.5.1.1
- UniProt
- P00805
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase 2 (EC 3.5.1.1) | protein | 303 | 32% helix, 22% strand | P00805 |
| B, D | L-asparaginase 2 (EC 3.5.1.1) | protein | 302 | 33% helix, 23% strand | P00805 |
| C | L-asparaginase 2 (EC 3.5.1.1) | protein | 305 | 33% helix, 22% strand | P00805 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.87 | 0.88 | 165 | empty |
| 2 | 86 | 0.73 | 0.96 | 25 | empty |
| 3 | 392 | 0.65 | 0.79 | 40 | empty |
| 4 | 378 | 0.63 | 0.79 | 39 | empty |
| 5 | 117 | 0.63 | 0.88 | 29 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2048 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2030 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 1004 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 975 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 766 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 P00805
- Elsewhere: RCSB PDB 6EOK · PDBe 6EOK · UniProt P00805
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