Research workbench
Wolinella succinogenes L-asparaginase S121 + L-aspartic acid, open conformation
Analyse Wolinella succinogenes L-asparaginase S121 + L-aspartic acid, open conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K4G
- Type
- protein
- Length
- 1,312 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase
- EC
- 3.5.1.1
- UniProt
- P50286
- Ligands
- ASP
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | L-asparaginase (EC 3.5.1.1) | protein | 328 | 32% helix, 20% strand | P50286 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.73 | 0.77 | 82 | empty |
| 2 | 147 | 0.68 | 0.89 | 38 | empty |
| 3 | 107 | 0.63 | 0.88 | 26 | empty |
| 4 | 222 | 0.52 | 0.77 | 28 | ASP |
| 5 | 207 | 0.50 | 0.76 | 29 | ASP |
Interfaces
4 interfaces between chains.
- A–B · 2055 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2045 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 237 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 42 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5K4G · Wolinella succinogenes L-asparaginase S121 + L-aspartic acid, open conformation · the same entry in another collection · chain D against D, TM-score 1.00
- P50286 · AlphaFold monomer V2.0 prediction for L-asparaginase (P50286) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P50286
- Elsewhere: RCSB PDB 5K4G · PDBe 5K4G · UniProt P50286
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