MolNFT v1 · #160085 · protein
E. COLI L-asparaginase II double mutant (T89V,K162T) in complex with L-asp at pH 7.0
6PA4 · L-asparaginase 2: “E. COLI L-asparaginase II double mutant (T89V,K162T) in complex with L-asp at pH 7.0”. X-ray diffraction, 1 ligand (ASP), 13 pockets (best druggability 0.65). MolNFT v1 #160085 on GenesisL1: 3D structure, binding…
- PDB
- 6PA4
- Type
- protein
- Length
- 1,264 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
- 13 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase 2 (EC 3.5.1.1) | protein | 321 | 34% helix, 23% strand | P00805 |
| B | L-asparaginase 2 (EC 3.5.1.1) | protein | 308 | 34% helix, 24% strand | P00805 |
| C | L-asparaginase 2 (EC 3.5.1.1) | protein | 323 | 34% helix, 23% strand | P00805 |
| D | L-asparaginase 2 (EC 3.5.1.1) | protein | 312 | 33% helix, 22% strand | P00805 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.65 | 0.88 | 29 | empty |
| 2 | 147 | 0.64 | 0.86 | 30 | empty |
| 3 | 214 | 0.53 | 0.78 | 28 | ASP |
| 4 | 111 | 0.50 | 0.81 | 24 | empty |
| 5 | 118 | 0.48 | 0.80 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2285 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 2255 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 244 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6PA4 · E. coli L-asparaginase II double mutant (T89V,K162T) in complex with L-Asp at pH 7.0 · the same entry in another collection · chain D against D, TM-score 1.00
- P00805 · AlphaFold monomer V2.0 prediction for L-asparaginase 2 (P00805) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 6PA4 · PDBe 6PA4 · UniProt P00805
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.