Research workbench
Structure of apo-cdd-1 beta-lactamase
Analyse Structure of apo-cdd-1 beta-lactamase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EDM
- Type
- protein
- Length
- 251 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A160YKM3
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 251 | 36% helix, 21% strand | A0A160YKM3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.42 | 0.74 | 30 | SO4 |
| 2 | 52 | 0.31 | 0.76 | 11 | empty |
Modifications
Observed in the structure: 1 modified (carboxylation).
Compared structures
- 6EDM · Structure of apo-CDD-1 beta-lactamase · 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 A0A160YKM3
- Elsewhere: RCSB PDB 6EDM · PDBe 6EDM · UniProt A0A160YKM3
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