Research workbench
The crystal structure of a beta-lactamase from legionella pneumophila str. paris
Analyse The crystal structure of a beta-lactamase from legionella pneumophila str. paris in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WHL
- Type
- protein
- Length
- 2,952 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A378KDC5
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Beta-lactamase (EC 3.5.2.6) | protein | 246 | 39% helix, 26% strand | A0A378KDC5 |
Ligands and binding sites
- GOL · Glycerol · additive · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.85 | 0.86 | 104 | GOL |
| 2 | 497 | 0.81 | 0.87 | 55 | GOL |
| 3 | 501 | 0.81 | 0.87 | 52 | GOL |
| 4 | 505 | 0.80 | 0.87 | 51 | GOL |
| 5 | 551 | 0.80 | 0.86 | 55 | GOL |
Interfaces
18 interfaces between chains.
- E–F · 1347 Ų buried · 20 hydrogen bonds · protein-protein
- K–L · 1325 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1321 Ų buried · 23 hydrogen bonds · protein-protein
- I–J · 1314 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 1309 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 modified, 6 disulfide (engineered, carboxylation, disulfide).
Compared structures
- 6WHL · The crystal structure of a beta-lactamase from Legionella pneumophila str. Paris · the same entry in another collection · chain A 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 A0A378KDC5
- Elsewhere: RCSB PDB 6WHL · PDBe 6WHL · UniProt A0A378KDC5
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