MolNFT v1 · #166834 · protein
Complex of double mutant (T89V,K162T) of E. COLI L-asparaginase II with L-asp
6V29 · L-asparaginase 2: “Complex of double mutant (T89V,K162T) of E. COLI L-asparaginase II with L-asp”. X-ray diffraction, 1 ligand (ASP), 10 pockets (best druggability 0.67). MolNFT v1 #166834 on GenesisL1: 3D structure, binding sites…
- PDB
- 6V29
- Type
- protein
- Length
- 1,239 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 0.67
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase 2 (EC 3.5.1.1) | protein | 311 | 35% helix, 22% strand | P00805 |
| B | L-asparaginase 2 (EC 3.5.1.1) | protein | 306 | 33% helix, 23% strand | P00805 |
| C | L-asparaginase 2 (EC 3.5.1.1) | protein | 312 | 35% helix, 22% strand | P00805 |
| D | L-asparaginase 2 (EC 3.5.1.1) | protein | 310 | 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 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.67 | 0.88 | 37 | empty |
| 2 | 131 | 0.66 | 0.88 | 30 | empty |
| 3 | 335 | 0.62 | 0.78 | 46 | ASP |
| 4 | 217 | 0.52 | 0.77 | 28 | ASP |
| 5 | 214 | 0.51 | 0.76 | 31 | ASP |
Interfaces
2 interfaces between chains.
- A–B · 2126 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 2106 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6V29 · Complex of double mutant (T89V,K162T) of E. coli L-asparaginase II with L-Asp · the same entry in another collection · chain B against B, TM-score 1.00
- P00805 · AlphaFold monomer V2.0 prediction for L-asparaginase 2 (P00805) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 6V29 · PDBe 6V29 · UniProt P00805
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