Research workbench
Crystal structure of yopt domain of pasteurella multocida PFHB2-toxin
Analyse Crystal structure of yopt domain of pasteurella multocida PFHB2-toxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U8T
- Type
- protein
- Length
- 854 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PFHB2
- UniProt
- Q9CPH9
- Ligands
- NA
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PFHB2 | protein | 211 | 39% helix, 28% strand | Q9CPH9 |
| C | PFHB2 | protein | 219 | 39% helix, 25% strand | Q9CPH9 |
| B | PFHB2 | protein | 221 | 42% helix, 27% strand | Q9CPH9 |
| D | PFHB2 | protein | 203 | 40% helix, 27% strand | Q9CPH9 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.73 | 0.82 | 85 | empty |
| 2 | 976 | 0.70 | 0.75 | 83 | empty |
| 3 | 341 | 0.69 | 0.82 | 66 | empty |
| 4 | 263 | 0.60 | 0.80 | 22 | empty |
| 5 | 264 | 0.56 | 0.77 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–B · 6148 Ų buried · 106 hydrogen bonds · protein-protein
- C–D · 6100 Ų buried · 110 hydrogen bonds · protein-protein
- A–C · 128 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 6U8T · Crystal structure of YopT domain of Pasteurella Multocida PfhB2-toxin · 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 Q9CPH9
- Elsewhere: RCSB PDB 6U8T · PDBe 6U8T · UniProt Q9CPH9
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