Research workbench
Metallo-beta-lactamase from Pontibacter korlensis
Analyse Metallo-beta-lactamase from Pontibacter korlensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XFR
- Type
- protein
- Length
- 431 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.608
- Source
- Pontibacter korlensis
- Molecule
- Lactamase_B domain-containing protein
- UniProt
- A0A0E3ZJD7
- Ligands
- ZN, NA, SO4
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · resolution 2.608 · 2 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lactamase_B domain-containing protein | protein | 215 | 25% helix, 33% strand | A0A0E3ZJD7 |
| B | Lactamase_B domain-containing protein | protein | 216 | 25% helix, 32% strand | A0A0E3ZJD7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 16 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 562 | 0.65 | 0.76 | 48 | EPE, NA |
| 2 | 108 | 0.56 | 0.84 | 21 | ZN, NA |
| 3 | 96 | 0.52 | 0.83 | 20 | ZN |
| 4 | 186 | 0.45 | 0.74 | 23 | SO4 |
Interfaces
1 interface between chains.
- A–B · 807 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6XFR · Metallo-beta-lactamase from pontibacter korlensis · 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 A0A0E3ZJD7
- Elsewhere: RCSB PDB 6XFR · PDBe 6XFR · UniProt A0A0E3ZJD7
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