MolNFT v1 · #166841 · protein
Complex of mutant (K162M) of E. COLI L-asparaginase II with L-asp. covalent acyl-enzyme intermediate and tetrahedral intermediate.
6V2G · L-asparaginase 2: “Complex of mutant (K162M) of E. COLI L-asparaginase II with L-asp. covalent acyl-enzyme intermediate and…”. X-ray diffraction, 10 pockets (best druggability 0.84). MolNFT v1 #166841 on GenesisL1: 3D structure…
- PDB
- 6V2G
- Type
- protein
- Length
- 1,306 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
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-asparaginase 2 (EC 3.5.1.1) | protein | 326 | 33% helix, 24% strand | P00805 |
| C, D | L-asparaginase 2 (EC 3.5.1.1) | protein | 327 | 33% helix, 24% strand | P00805 |
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.84 | 0.90 | 97 | empty |
| 2 | 298 | 0.80 | 0.91 | 56 | empty |
| 3 | 143 | 0.77 | 0.95 | 32 | empty |
| 4 | 131 | 0.76 | 0.95 | 33 | empty |
| 5 | 81 | 0.71 | 0.95 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2436 Ų buried · 59 hydrogen bonds · protein-protein
- B–D · 2426 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 1089 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1074 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1046 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 modified (disulfide, nonstandard).
Compared structures
- 6V2G · Complex of mutant (K162M) of E. coli L-asparaginase II with L-Asp. Covalent acyl-enzyme… · 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 D 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 6V2G · PDBe 6V2G · UniProt P00805
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