Research workbench
Crystal structure of wild type class D beta-lactamase from clostridium difficile 630
Analyse Crystal structure of wild type class D beta-lactamase from clostridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WY4
- Type
- protein
- Length
- 1,004 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
- NA
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 248 | 37% helix, 21% strand | Q188Q3 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 248 | 37% helix, 19% strand | Q188Q3 |
| C, D | Beta-lactamase (EC 3.5.2.6) | protein | 254 | 34% helix, 19% strand | Q188Q3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.77 | 0.84 | 56 | empty |
| 2 | 110 | 0.55 | 0.84 | 14 | empty |
| 3 | 85 | 0.50 | 0.83 | 17 | empty |
| 4 | 159 | 0.45 | 0.76 | 26 | empty |
| 5 | 170 | 0.45 | 0.75 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 454 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 274 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 200 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 141 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 100 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 6WY4 · Crystal Structure of Wild Type 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 6WY4 · PDBe 6WY4 · UniProt Q188Q3
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