Research workbench
Crystal structure of dimeric latent PorU from Porphyromonas gingivalis
Analyse Crystal structure of dimeric latent PorU from Porphyromonas gingivalis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZA2
- Type
- protein
- Length
- 2,164 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.35
- Source
- Porphyromonas gingivalis ATCC 33277
- Molecule
- Por secretion system protein porU
- UniProt
- B2RGP6
- Ligands
- CA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · resolution 3.35 · 2 distinct chains · 13% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Por secretion system protein porU | protein | 1081 | 14% helix, 40% strand | B2RGP6 |
| B | Por secretion system protein porU | protein | 1083 | 13% helix, 40% strand | B2RGP6 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.86 | 0.87 | 106 | empty |
| 2 | 259 | 0.80 | 0.92 | 50 | empty |
| 3 | 259 | 0.74 | 0.88 | 25 | empty |
| 4 | 108 | 0.74 | 0.95 | 26 | empty |
| 5 | 383 | 0.73 | 0.84 | 60 | empty |
Interfaces
1 interface between chains.
- A–B · 3462 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 6ZA2 · Crystal structure of dimeric latent poru from porphyromonas gingivalis · 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 B2RGP6
- Elsewhere: RCSB PDB 6ZA2 · PDBe 6ZA2 · UniProt B2RGP6
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