MolNFT v1 · #124074 · protein
Wolinella succinogenes L-asparaginase S121 + L-glutamic acid
5K4H: “Wolinella succinogenes L-asparaginase S121 + L-glutamic acid”. X-ray diffraction, 1 ligand (GLU), 20 pockets (best druggability 0.83). MolNFT v1 #124074 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5K4H
- Type
- protein
- Length
- 2,580 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-asparaginase
- EC
- 3.5.1.1
- UniProt
- P50286
- Ligands
- GLU
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | L-asparaginase (EC 3.5.1.1) | protein | 328 | 33% helix, 21% strand | P50286 |
| B | L-asparaginase (EC 3.5.1.1) | protein | 320 | 33% helix, 22% strand | P50286 |
| C | L-asparaginase (EC 3.5.1.1) | protein | 316 | 33% helix, 23% strand | P50286 |
| D | L-asparaginase (EC 3.5.1.1) | protein | 319 | 33% helix, 22% strand | P50286 |
| E | L-asparaginase (EC 3.5.1.1) | protein | 321 | 33% helix, 22% strand | P50286 |
| F | L-asparaginase (EC 3.5.1.1) | protein | 322 | 33% helix, 22% strand | P50286 |
| H | L-asparaginase (EC 3.5.1.1) | protein | 326 | 32% helix, 22% strand | P50286 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
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 | 682 | 0.83 | 0.88 | 109 | empty |
| 2 | 102 | 0.75 | 0.96 | 41 | empty |
| 3 | 326 | 0.72 | 0.85 | 51 | empty |
| 4 | 751 | 0.71 | 0.78 | 70 | GLU |
| 5 | 73 | 0.68 | 0.95 | 31 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2062 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2059 Ų buried · 40 hydrogen bonds · protein-protein
- G–H · 2053 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2042 Ų buried · 42 hydrogen bonds · protein-protein
- E–G · 949 Ų buried · 8 hydrogen bonds · protein-protein
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 P50286
- Elsewhere: RCSB PDB 5K4H · PDBe 5K4H · UniProt P50286
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