Research workbench
1.85 ångström resolution crystal structure of class D beta-lactamase from clostridium difficile 630
Analyse 1.85 ångström resolution crystal structure of class D beta-lactamase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UE2
- Type
- protein
- Length
- 1,007 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
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 4 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 | 249 | 37% helix, 19% strand | Q188Q3 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 254 | 36% helix, 20% strand | Q188Q3 |
| D | Beta-lactamase (EC 3.5.2.6) | protein | 255 | 36% helix, 18% strand | Q188Q3 |
Ligands and binding sites
- PGE · Triethylene glycol · additive · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains B
- PPI · Propanoic acid · additive · chains A, C
- GOL · Glycerol · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.79 | 0.81 | 133 | empty |
| 2 | 144 | 0.56 | 0.82 | 17 | empty |
| 3 | 227 | 0.50 | 0.75 | 38 | empty |
| 4 | 199 | 0.49 | 0.75 | 33 | empty |
| 5 | 76 | 0.45 | 0.82 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–B · 459 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 275 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 192 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 137 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 127 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered, carboxylation).
Compared structures
- 6UE2 · 1.85 Angstrom Resolution Crystal Structure of Class D beta-lactamase from Clostridium… · 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 6UE2 · PDBe 6UE2 · UniProt Q188Q3
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