MolNFT v1 · #160086 · protein
ECAII(T89V,K162T) mutant in complex with L-asn at pH 8.3 in space group P2(1)
6PA5 · L-asparaginase 2: “ECAII(T89V,K162T) mutant in complex with L-asn at pH 8.3 in space group P2(1)”. X-ray diffraction, 1 ligand (ASN), 20 pockets (best druggability 0.83). MolNFT v1 #160086 on GenesisL1: 3D structure, binding sites…
- PDB
- 6PA5
- Type
- protein
- Length
- 2,558 residues
- Chains
- 8
- 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
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G, H | L-asparaginase 2 (EC 3.5.1.1) | protein | 326 | 34% helix, 23% strand | P00805 |
| C, D | L-asparaginase 2 (EC 3.5.1.1) | protein | 314 | 34% helix, 24% strand | P00805 |
| E, F | L-asparaginase 2 (EC 3.5.1.1) | protein | 313 | 35% helix, 24% strand | P00805 |
Ligands and binding sites
- ASN · Asparagine · ligand · 8 copies · chains A, C, B, D, E, G, F, H
- IMD · Imidazole · additive · 7 copies · chains A, B, C, D, E, F, G
- GOL · Glycerol · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.83 | 0.91 | 104 | ASN |
| 2 | 458 | 0.82 | 0.89 | 92 | empty |
| 3 | 180 | 0.79 | 0.95 | 37 | ASN |
| 4 | 174 | 0.79 | 0.95 | 39 | ASN |
| 5 | 169 | 0.79 | 0.95 | 37 | ASN |
Interfaces
15 interfaces between chains.
- A–C · 2287 Ų buried · 43 hydrogen bonds · protein-protein
- B–D · 2285 Ų buried · 43 hydrogen bonds · protein-protein
- E–G · 2282 Ų buried · 49 hydrogen bonds · protein-protein
- F–H · 2278 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 1035 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6PA5 · ECAII(T89V,K162T) mutant in complex with L-asn at pH 8.3 in space group P2(1) · the same entry in another collection · chain H against H, 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 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 6PA5 · PDBe 6PA5 · UniProt P00805
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