Research workbench
Crystal structure of DCTP7, a bordetella pertussis extracytoplasmic solute receptor binding pyroglutamic acid
Analyse Crystal structure of DCTP7, a bordetella pertussis extracytoplasmic solute… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PFY
- Type
- protein
- Length
- 1,204 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative exported protein
- UniProt
- Q7VXB1
- Ligands
- PCA
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative exported protein | protein | 301 | 53% helix, 19% strand | Q7VXB1 |
Ligands and binding sites
- PCA · Pyroglutamic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.79 | 0.83 | 119 | empty |
| 2 | 780 | 0.71 | 0.77 | 88 | empty |
| 3 | 377 | 0.63 | 0.78 | 40 | empty |
| 4 | 419 | 0.60 | 0.76 | 51 | empty |
| 5 | 106 | 0.47 | 0.80 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–C · 863 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 845 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 710 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 696 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 283 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 2PFY · Crystal structure of DctP7, a Bordetella pertussis extracytoplasmic solute receptor… · the same entry in another collection · chain B against B, 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 Q7VXB1
- Elsewhere: RCSB PDB 2PFY · PDBe 2PFY · UniProt Q7VXB1
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