MolNFT v1 · #186654 · protein
Crystal structure of C79A mutant of class D beta-lactamase from clostridium difficile 630
7RL8: “Crystal structure of C79A mutant of class D beta-lactamase from clostridium difficile 630”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.75). MolNFT v1 #186654 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7RL8
- Type
- protein
- Length
- 1,005 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q188Q3
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 249 | 37% helix, 20% strand | Q188Q3 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 248 | 38% helix, 19% strand | Q188Q3 |
| C, D | Beta-lactamase (EC 3.5.2.6) | protein | 254 | 36% helix, 19% strand | Q188Q3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 861 | 0.75 | 0.79 | 85 | empty |
| 2 | 988 | 0.73 | 0.76 | 68 | empty |
| 3 | 423 | 0.61 | 0.76 | 51 | PEG |
| 4 | 203 | 0.50 | 0.76 | 35 | SO4 |
| 5 | 199 | 0.49 | 0.76 | 32 | empty |
Interfaces
5 interfaces between chains.
- A–B · 462 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 270 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 198 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 132 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 7RL8 · Crystal Structure of C79A Mutant of Class D beta-lactamase from Clostridium difficile 630 · 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 Q188Q3
- Elsewhere: RCSB PDB 7RL8 · PDBe 7RL8 · UniProt Q188Q3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.