Research workbench
Crystal structure of the class B3 di-zinc metallo-beta-lactamase lra- 12 from an alaskan soil metagenome.
Analyse Crystal structure of the class B3 di-zinc metallo-beta-lactamase lra- 12 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AEB
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lra-12
- EC
- 3.5.2.6
- UniProt
- B5L5V5
- Ligands
- ZN, CO, SO4
- Pockets
- 3 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lra-12 (EC 3.5.2.6) | protein | 264 | 32% helix, 24% strand | B5L5V5 |
| B | Lra-12 (EC 3.5.2.6) | protein | 266 | 32% helix, 24% strand | B5L5V5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CO · Cobalt (II) ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.38 | 0.75 | 25 | ZN |
| 2 | 131 | 0.38 | 0.73 | 23 | empty |
| 3 | 79 | 0.31 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 161 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5AEB · Crystal structure of the class B3 di-zinc metallo-beta-lactamase LRA- 12 from an Alaskan… · 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 B5L5V5
- Elsewhere: RCSB PDB 5AEB · PDBe 5AEB · UniProt B5L5V5
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