Research workbench
1.8 ångström crystal structure of the periplasmic domain of the membrane insertase yidc
Analyse 1.8 ångström crystal structure of the periplasmic domain of the membrane… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BS6
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inner membrane protein oxaa
- UniProt
- P25714
- Ligands
- CA
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inner membrane protein oxaa | protein | 258 | 7% helix, 55% strand | P25714 |
| B | Inner membrane protein oxaa | protein | 260 | 7% helix, 54% strand | P25714 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- PGE · Triethylene glycol · additive · 3 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
- 2PE · Nonaethylene glycol · additive · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.77 | 0.80 | 112 | PGE, EDO |
| 2 | 183 | 0.46 | 0.75 | 29 | empty |
| 3 | 62 | 0.32 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 599 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3BS6 · 1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase 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 0.99
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 3BS6 · PDBe 3BS6 · UniProt P25714
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