Research workbench
Crystal structure of minor pilin cofb from CFA/III complexed with N- terminal peptide fragment of cofj
Analyse Crystal structure of minor pilin cofb from CFA/III complexed with N- terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YPZ
- Type
- protein
- Length
- 1,473 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cofb; Cofj
- UniProt
- Q93I73, Q93I65
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Cofb | protein | 480 | 12% helix, 39% strand | Q93I73 |
| D, E, F | Cofj | protein | 11 | 0% helix, 45% strand | Q93I65 |
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.77 | 0.79 | 111 | empty |
| 2 | 74 | 0.75 | 0.98 | 18 | empty |
| 3 | 964 | 0.72 | 0.76 | 64 | empty |
| 4 | 309 | 0.63 | 0.80 | 40 | empty |
| 5 | 286 | 0.62 | 0.80 | 38 | empty |
Interfaces
9 interfaces between chains.
- B–C · 4443 Ų buried · 63 hydrogen bonds · protein-protein
- A–C · 4176 Ų buried · 67 hydrogen bonds · protein-protein
- A–B · 4138 Ų buried · 72 hydrogen bonds · protein-protein
- B–F · 619 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 588 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5YPZ · Crystal structure of minor pilin CofB from CFA/III complexed with N-terminal peptide… · 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 Q93I73
- Every structure of UniProt Q93I65
- Elsewhere: RCSB PDB 5YPZ · PDBe 5YPZ · UniProt Q93I73 · UniProt Q93I65
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