Research workbench
Crystal structure of the periplasmic domain of the escherichia COLI yidc
Analyse Crystal structure of the periplasmic domain of the escherichia COLI yidc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BLC
- Type
- protein
- Length
- 558 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inner membrane protein oxaa
- UniProt
- P25714
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inner membrane protein oxaa | protein | 280 | 9% helix, 49% strand | P25714 |
| B | Inner membrane protein oxaa | protein | 278 | 9% helix, 49% strand | P25714 |
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 | 802 | 0.74 | 0.78 | 48 | empty |
| 2 | 222 | 0.50 | 0.75 | 28 | empty |
| 3 | 62 | 0.28 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 885 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3BLC · Crystal structure of the periplasmic domain of the Escherichia Coli YIDC · the same entry in another collection · chain A against A, TM-score 1.00
- P25714 · AlphaFold monomer V2.0 prediction for membrane protein insertase yidc (P25714) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P25714
- Elsewhere: RCSB PDB 3BLC · PDBe 3BLC · UniProt P25714
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