Research workbench
Crystal structure of the major pseudopilin from the type 2 secretion system of vibrio vulnificus
Analyse Crystal structure of the major pseudopilin from the type 2 secretion system of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GN9
- Type
- protein
- Length
- 335 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II secretory pathway, pseudopilin epsg
- UniProt
- Q8DDT3
- Ligands
- MLT, CA
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Type II secretory pathway, pseudopilin epsg | protein | 112 | 35% helix, 10% strand | Q8DDT3 |
| C | Type II secretory pathway, pseudopilin epsg | protein | 111 | 31% helix, 10% strand | Q8DDT3 |
Ligands and binding sites
- MLT · D-malate · ligand · 2 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.75 | 0.96 | 33 | MLT |
| 2 | 319 | 0.64 | 0.80 | 54 | empty |
Interfaces
3 interfaces between chains.
- B–C · 471 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 467 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 466 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3GN9 · Crystal structure of the major pseudopilin from the type 2 secretion system of Vibrio… · 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 Q8DDT3
- Elsewhere: RCSB PDB 3GN9 · PDBe 3GN9 · UniProt Q8DDT3
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