MolNFT v1 · #115897 · protein
Structure of ragb, a major immunodominant virulence factor of porphyromonas gingivalis.
5CX8 · Lipoprotein ragb: “Structure of ragb, a major immunodominant virulence factor of porphyromonas gingivalis.”. X-ray diffraction, 3 ligands (3DO, TG6, RP3), 10 pockets (best druggability 0.82). MolNFT v1 #115897 on GenesisL1: 3D…
- PDB
- 5CX8
- Type
- protein
- Length
- 944 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipoprotein ragb
- UniProt
- F5H948
- Ligands
- 3DO, TG6, RP3
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lipoprotein ragb | protein | 472 | 45% helix, 10% strand | F5H948 |
Ligands and binding sites
- 3DO · 3-deoxy-beta-D-glucopyranose · ligand · chains A, B
- TG6 · 6-O-phosphono-D-tagatose · ligand · chains A
- RP3 · 3-deoxy-5-O-phosphono-beta-D-ribofuranose · ligand · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.82 | 0.84 | 78 | 3DO, RP3 |
| 2 | 169 | 0.81 | 0.96 | 36 | empty |
| 3 | 163 | 0.80 | 0.97 | 35 | empty |
| 4 | 169 | 0.72 | 0.90 | 34 | empty |
| 5 | 155 | 0.70 | 0.90 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 621 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 5CX8 · Structure of RagB, a major immunodominant virulence factor of 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 F5H948
- Elsewhere: RCSB PDB 5CX8 · PDBe 5CX8 · UniProt F5H948
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