MolNFT v1 · #160093 · protein
E. COLI L-asparaginase II in complex with L-asp at pH 5.6
6PAC · L-asparaginase 2: “E. COLI L-asparaginase II in complex with L-asp at pH 5.6”. X-ray diffraction, 1 ligand (ASP), 11 pockets (best druggability 0.67). MolNFT v1 #160093 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6PAC
- Type
- protein
- Length
- 1,292 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 0.67
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 | 330 | 33% helix, 23% strand | P00805 |
| B | L-asparaginase 2 (EC 3.5.1.1) | protein | 318 | 34% helix, 24% strand | P00805 |
| C | L-asparaginase 2 (EC 3.5.1.1) | protein | 328 | 34% helix, 23% strand | P00805 |
| D | L-asparaginase 2 (EC 3.5.1.1) | protein | 316 | 34% helix, 23% strand | P00805 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 4 copies · chains A, B, C, D
- IMD · Imidazole · additive · 2 copies · chains 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.67 | 0.89 | 29 | empty |
| 2 | 145 | 0.65 | 0.87 | 31 | empty |
| 3 | 335 | 0.56 | 0.75 | 49 | empty |
| 4 | 126 | 0.53 | 0.82 | 35 | ASP |
| 5 | 130 | 0.52 | 0.81 | 31 | ASP |
Interfaces
3 interfaces between chains.
- C–D · 2300 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2257 Ų buried · 48 hydrogen bonds · protein-protein
- A–C · 259 Ų buried · 4 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 6PAC · PDBe 6PAC · UniProt P00805
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