MolNFT v1 · #181647 · protein
L-asparaginase from escherichia COLI with bound aspartic acid
7M11 · L-asparaginase 2: “L-asparaginase from escherichia COLI with bound aspartic acid”. X-ray diffraction, 1 ligand (ASP), 10 pockets (best druggability 0.78). MolNFT v1 #181647 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7M11
- Type
- protein
- Length
- 1,231 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
- 10 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase 2 (EC 3.5.1.1) | protein | 308 | 32% helix, 24% strand | P00805 |
| B | L-asparaginase 2 (EC 3.5.1.1) | protein | 302 | 34% helix, 23% strand | P00805 |
| C | L-asparaginase 2 (EC 3.5.1.1) | protein | 326 | 33% helix, 24% strand | P00805 |
| D | L-asparaginase 2 (EC 3.5.1.1) | protein | 295 | 32% helix, 23% 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
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.78 | 0.95 | 35 | ASP |
| 2 | 254 | 0.75 | 0.89 | 50 | empty |
| 3 | 175 | 0.72 | 0.90 | 48 | empty |
| 4 | 165 | 0.71 | 0.90 | 40 | empty |
| 5 | 296 | 0.67 | 0.82 | 45 | ASP |
Interfaces
6 interfaces between chains.
- C–D · 2305 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2194 Ų buried · 47 hydrogen bonds · protein-protein
- B–D · 1073 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1013 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 923 Ų buried · 12 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 7M11 · PDBe 7M11 · UniProt P00805
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