MolNFT v1 · #160084 · protein
E. COLI L-asparaginase II double mutant (T89V,K162T) in complex with L-asn at pH 7.0
6PA3 · L-asparaginase 2: “E. COLI L-asparaginase II double mutant (T89V,K162T) in complex with L-asn at pH 7.0”. X-ray diffraction, 2 ligands (ASN, MG), 12 pockets (best druggability 0.70). MolNFT v1 #160084 on GenesisL1: 3D structure…
- PDB
- 6PA3
- Type
- protein
- Length
- 1,322 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, MG
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase 2 (EC 3.5.1.1) | protein | 334 | 33% helix, 23% strand | P00805 |
| B, C | L-asparaginase 2 (EC 3.5.1.1) | protein | 328 | 33% helix, 24% strand | P00805 |
| D | L-asparaginase 2 (EC 3.5.1.1) | protein | 332 | 34% helix, 23% strand | P00805 |
Ligands and binding sites
- ASN · Asparagine · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains A
- IMD · Imidazole · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.70 | 0.88 | 40 | empty |
| 2 | 146 | 0.68 | 0.89 | 37 | empty |
| 3 | 422 | 0.60 | 0.76 | 53 | empty |
| 4 | 120 | 0.60 | 0.86 | 27 | ASN |
| 5 | 145 | 0.58 | 0.83 | 35 | ASN |
Interfaces
3 interfaces between chains.
- A–B · 2434 Ų buried · 54 hydrogen bonds · protein-protein
- C–D · 2391 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 275 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6PA3 · E. coli L-asparaginase II double mutant (T89V,K162T) in complex with L-Asn at pH 7.0 · 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 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 6PA3 · PDBe 6PA3 · UniProt P00805
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