Research workbench
Secreted chlamydial protein PGP3, full-length
Analyse Secreted chlamydial protein PGP3, full-length in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JDM
- Type
- protein
- Length
- 1,590 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virulence plasmid protein PGP3-D
- UniProt
- D7DHH5
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Virulence plasmid protein PGP3-D | protein | 263 | 14% helix, 41% strand | D7DHH5 |
| B, E | Virulence plasmid protein PGP3-D | protein | 263 | 14% helix, 43% strand | D7DHH5 |
| C, F | Virulence plasmid protein PGP3-D | protein | 269 | 15% helix, 42% strand | D7DHH5 |
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.79 | 0.87 | 46 | empty |
| 2 | 117 | 0.79 | 0.98 | 29 | empty |
| 3 | 125 | 0.77 | 0.96 | 29 | empty |
| 4 | 473 | 0.76 | 0.84 | 45 | empty |
| 5 | 149 | 0.67 | 0.88 | 37 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3289 Ų buried · 34 hydrogen bonds · protein-protein
- D–F · 3262 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 3247 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 3238 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 3212 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 4JDM · Secreted Chlamydial Protein PGP3, full-length · 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 D7DHH5
- Elsewhere: RCSB PDB 4JDM · PDBe 4JDM · UniProt D7DHH5
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