MolNFT v1 · #160089 · protein
ECAII(T89V,K162T) mutant in complex with L-asn at pH 7.0
6PA8 · L-asparaginase 2: “ECAII(T89V,K162T) mutant in complex with L-asn at pH 7.0”. X-ray diffraction, 2 ligands (ASN, MG), 11 pockets (best druggability 0.66). MolNFT v1 #160089 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6PA8
- Type
- protein
- Length
- 1,305 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
- 11 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-asparaginase 2 (EC 3.5.1.1) | protein | 331 | 33% helix, 23% strand | P00805 |
| B | L-asparaginase 2 (EC 3.5.1.1) | protein | 316 | 34% helix, 24% strand | P00805 |
| C | L-asparaginase 2 (EC 3.5.1.1) | protein | 330 | 34% helix, 23% strand | P00805 |
| D | L-asparaginase 2 (EC 3.5.1.1) | protein | 328 | 33% helix, 23% strand | P00805 |
Ligands and binding sites
- ASN · Asparagine · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B, C
- IMD · Imidazole · additive · 2 copies · chains A, C
- FLC · Citrate anion · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.66 | 0.87 | 29 | empty |
| 2 | 128 | 0.65 | 0.88 | 28 | empty |
| 3 | 115 | 0.60 | 0.86 | 26 | ASN |
| 4 | 371 | 0.57 | 0.75 | 45 | empty |
| 5 | 128 | 0.55 | 0.83 | 33 | ASN |
Interfaces
3 interfaces between chains.
- C–D · 2385 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 2314 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 271 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 6PA8 · PDBe 6PA8 · UniProt P00805
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