MolNFT v1 · #11327 · protein
Crystal structure of orthorhombic form of D90E mutant of escherichia COLI L-asparaginase II
1JJA: “Crystal structure of orthorhombic form of D90E mutant of escherichia COLI L-asparaginase II”. X-ray diffraction, 17 pockets (best druggability 0.81). MolNFT v1 #11327 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1JJA
- Type
- protein
- Length
- 1,873 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase II
- EC
- 3.5.1.1
- UniProt
- P00805
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase II (EC 3.5.1.1) | protein | 309 | 32% helix, 22% strand | P00805 |
| B | L-asparaginase II (EC 3.5.1.1) | protein | 304 | 32% helix, 23% strand | P00805 |
| C | L-asparaginase II (EC 3.5.1.1) | protein | 326 | 36% helix, 21% strand | P00805 |
| D, E | L-asparaginase II (EC 3.5.1.1) | protein | 307 | 31% helix, 22% strand | P00805 |
| F | L-asparaginase II (EC 3.5.1.1) | protein | 320 | 31% helix, 21% strand | P00805 |
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.81 | 0.89 | 86 | empty |
| 2 | 932 | 0.74 | 0.78 | 88 | empty |
| 3 | 86 | 0.74 | 0.96 | 26 | empty |
| 4 | 87 | 0.71 | 0.95 | 25 | empty |
| 5 | 118 | 0.67 | 0.90 | 28 | empty |
Interfaces
9 interfaces between chains.
- E–F · 2085 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 2075 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 2063 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 1003 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 961 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1JJA · Crystal structure of orthorhombic form of D90E mutant of escherichia COLI L-asparaginase… · the same entry in another collection · chain F against F, TM-score 1.00
- P00805 · AlphaFold monomer V2.0 prediction for L-asparaginase 2 (P00805) · 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 P00805
- Elsewhere: RCSB PDB 1JJA · PDBe 1JJA · UniProt P00805
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