MolNFT v1 · #160083 · protein
E. COLI L-asparaginase II mutant (K162M) in complex with L-asp at pH 5.6
6PA2 · L-asparaginase 2: “E. COLI L-asparaginase II mutant (K162M) in complex with L-asp at pH 5.6”. X-ray diffraction, 1 ligand (ASP), 7 pockets (best druggability 0.83). MolNFT v1 #160083 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6PA2
- Type
- protein
- Length
- 1,263 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
- 7 · best druggability 0.83
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 | 35% helix, 24% strand | P00805 |
| C | L-asparaginase 2 (EC 3.5.1.1) | protein | 311 | 34% helix, 24% strand | P00805 |
| B | L-asparaginase 2 (EC 3.5.1.1) | protein | 327 | 33% helix, 23% strand | P00805 |
| D | L-asparaginase 2 (EC 3.5.1.1) | protein | 312 | 34% helix, 24% strand | P00805 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.83 | 0.90 | 107 | empty |
| 2 | 245 | 0.80 | 0.93 | 54 | empty |
| 3 | 90 | 0.72 | 0.95 | 31 | empty |
| 4 | 143 | 0.69 | 0.90 | 37 | empty |
| 5 | 117 | 0.66 | 0.90 | 40 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2320 Ų buried · 51 hydrogen bonds · protein-protein
- A–C · 2148 Ų buried · 45 hydrogen bonds · protein-protein
- A–D · 1047 Ų buried · 19 hydrogen bonds · protein-protein
- C–B · 1030 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 903 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6PA2 · E. coli L-asparaginase II mutant (K162M) in complex with L-Asp at pH 5.6 · 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 6PA2 · PDBe 6PA2 · UniProt P00805
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