MolNFT v1 · #59245 · protein
1.8 ångström crystal structure of the periplasmic domain of the membrane insertase yidc
3BS6 · Inner membrane protein oxaa: “1.8 ångström crystal structure of the periplasmic domain of the membrane insertase yidc”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.77). MolNFT v1 #59245 on GenesisL1: 3D…
- 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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