MolNFT v1 · #188694 · protein
Albumin binding domain fused to a mutant of the erwinia asparaginase
7U6M · L-asparaginase: “Albumin binding domain fused to a mutant of the erwinia asparaginase”. X-ray diffraction, 1 ligand (ASP), 15 pockets (best druggability 0.86). MolNFT v1 #188694 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7U6M
- Type
- protein
- Length
- 1,323 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase
- EC
- 3.5.1.1
- UniProt
- P06608
- Ligands
- ASP
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | L-asparaginase (EC 3.5.1.1) | protein | 327 | 32% helix, 24% strand | P06608 |
| C | L-asparaginase (EC 3.5.1.1) | protein | 342 | 31% helix, 24% strand | P06608 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 474 | 0.86 | 0.93 | 82 | empty |
| 2 | 306 | 0.78 | 0.89 | 48 | ASP |
| 3 | 270 | 0.75 | 0.88 | 45 | ASP |
| 4 | 254 | 0.74 | 0.88 | 40 | ASP |
| 5 | 247 | 0.73 | 0.87 | 46 | ASP |
Interfaces
6 interfaces between chains.
- A–C · 2405 Ų buried · 44 hydrogen bonds · protein-protein
- B–D · 2398 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 1126 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1115 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1088 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 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 P06608
- Elsewhere: RCSB PDB 7U6M · PDBe 7U6M · UniProt P06608
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