Research workbench
Structural and functional probing of porz, an essential bacterial surface component of the type-IX secretion system of human oral- microbiomic porphyromonas gingivalis.
Analyse Structural and functional probing of porz, an essential bacterial surface… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M11
- Type
- protein
- Length
- 748 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoreactive 84KD antigen PG93
- UniProt
- Q9S3Q8
- Ligands
- ZN, CA, CL
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoreactive 84KD antigen PG93 | protein | 748 | 3% helix, 47% strand | Q9S3Q8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A
- CA · Calcium ion · metal · 4 copies · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- CAC · Cacodylate ion · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.73 | 0.82 | 57 | GOL |
| 2 | 594 | 0.71 | 0.79 | 53 | ZN, GOL |
| 3 | 68 | 0.39 | 0.79 | 18 | empty |
| 4 | 84 | 0.31 | 0.73 | 22 | PEG |
| 5 | 69 | 0.30 | 0.74 | 16 | empty |
Compared structures
- 5M11 · Structural and functional probing of PorZ, an essential bacterial surface component of… · 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 Q9S3Q8
- Elsewhere: RCSB PDB 5M11 · PDBe 5M11 · UniProt Q9S3Q8
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