MolNFT v1 · #96228 · protein
Secreted chlamydial protein PGP3, C-terminal domain
4JDN · Virulence plasmid protein PGP3-D: “Secreted chlamydial protein PGP3, C-terminal domain”. X-ray diffraction, 1 ligand (K), 6 pockets (best druggability 0.79). MolNFT v1 #96228 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4JDN
- Type
- protein
- Length
- 434 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virulence plasmid protein PGP3-D
- UniProt
- D7DHH5
- Ligands
- K
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 1% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Virulence plasmid protein PGP3-D | protein | 144 | 0% helix, 55% strand | D7DHH5 |
| B | Virulence plasmid protein PGP3-D | protein | 143 | 2% helix, 53% strand | D7DHH5 |
| C | Virulence plasmid protein PGP3-D | protein | 147 | 2% helix, 52% strand | D7DHH5 |
Ligands and binding sites
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 | 155 | 0.79 | 0.96 | 39 | empty |
| 2 | 68 | 0.74 | 0.99 | 25 | empty |
| 3 | 200 | 0.48 | 0.75 | 23 | empty |
| 4 | 98 | 0.45 | 0.79 | 25 | empty |
| 5 | 83 | 0.41 | 0.78 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1058 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 979 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 975 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4JDN · Secreted Chlamydial Protein PGP3, C-terminal Domain · 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 4JDN · PDBe 4JDN · UniProt D7DHH5
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