MolNFT v1 · #160091 · protein
E. COLI L-asparaginase II mutant (T12V) in complex with L-asp at pH 5.5
6PAA · L-asparaginase 2: “E. COLI L-asparaginase II mutant (T12V) in complex with L-asp at pH 5.5”. X-ray diffraction, 1 ligand (ASP), 11 pockets (best druggability 0.66). MolNFT v1 #160091 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6PAA
- Type
- protein
- Length
- 1,243 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
- ASP
- Pockets
- 11 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase 2 (EC 3.5.1.1) | protein | 313 | 36% helix, 24% strand | P00805 |
| B | L-asparaginase 2 (EC 3.5.1.1) | protein | 304 | 33% helix, 25% strand | P00805 |
| C | L-asparaginase 2 (EC 3.5.1.1) | protein | 314 | 35% helix, 24% strand | P00805 |
| D | L-asparaginase 2 (EC 3.5.1.1) | protein | 312 | 33% helix, 24% strand | P00805 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.66 | 0.89 | 31 | empty |
| 2 | 140 | 0.64 | 0.87 | 29 | empty |
| 3 | 90 | 0.52 | 0.84 | 32 | empty |
| 4 | 100 | 0.43 | 0.79 | 26 | ASP |
| 5 | 97 | 0.42 | 0.78 | 24 | ASP |
Interfaces
2 interfaces between chains.
- A–B · 2115 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2114 Ų buried · 43 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 6PAA · PDBe 6PAA · UniProt P00805
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