Research workbench
Crystal structure of C-terminal domain of putative exported cytochrome C biogenesis-related protein from bacteroides fragilis
Analyse Crystal structure of C-terminal domain of putative exported cytochrome C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F9U
- Type
- protein
- Length
- 293 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative exported cytochrome C biogenesis-related protein
- UniProt
- Q5LAZ4
- Ligands
- NO3
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative exported cytochrome C biogenesis-related protein | protein | 145 | 42% helix, 26% strand | Q5LAZ4 |
| B | Putative exported cytochrome C biogenesis-related protein | protein | 148 | 41% helix, 25% strand | Q5LAZ4 |
Ligands and binding sites
- NO3 · Nitrate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.76 | 0.90 | 48 | NO3, EDO |
| 2 | 349 | 0.71 | 0.83 | 37 | empty |
| 3 | 75 | 0.39 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1036 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3F9U · Crystal structure of C-terminal domain of putative exported cytochrome C… · 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 Q5LAZ4
- Elsewhere: RCSB PDB 3F9U · PDBe 3F9U · UniProt Q5LAZ4
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