MolNFT v1 · #160087 · protein
ECAII(T89V,K162T) mutant in complex with L-asn at pH 8.3 in space group C2
6PA6 · L-asparaginase 2: “ECAII(T89V,K162T) mutant in complex with L-asn at pH 8.3 in space group C2”. X-ray diffraction, 1 ligand (ASN), 10 pockets (best druggability 0.56). MolNFT v1 #160087 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6PA6
- Type
- protein
- Length
- 1,278 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
- ASN
- Pockets
- 10 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | L-asparaginase 2 (EC 3.5.1.1) | protein | 326 | 34% helix, 23% strand | P00805 |
| B | L-asparaginase 2 (EC 3.5.1.1) | protein | 312 | 35% helix, 24% strand | P00805 |
| D | L-asparaginase 2 (EC 3.5.1.1) | protein | 314 | 34% helix, 24% strand | P00805 |
Ligands and binding sites
- ASN · Asparagine · ligand · 4 copies · chains A, B, C, D
- IMD · Imidazole · additive · 3 copies · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.56 | 0.75 | 53 | empty |
| 2 | 123 | 0.56 | 0.83 | 32 | ASN |
| 3 | 85 | 0.53 | 0.85 | 21 | empty |
| 4 | 119 | 0.53 | 0.82 | 25 | empty |
| 5 | 95 | 0.49 | 0.82 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2301 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 2292 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 258 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6PA6 · ECAII(T89V,K162T) MUTANT IN COMPLEX WITH L-ASN AT PH 8.3 in space group C2 · the same entry in another collection · chain C against C, TM-score 1.00
- P00805 · AlphaFold monomer V2.0 prediction for L-asparaginase 2 (P00805) · a predicted model of the same protein · chain C 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 6PA6 · PDBe 6PA6 · UniProt P00805
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