Research workbench
Crystal structure of the periplasmic domain of the thermotoga maritima yidc
Analyse Crystal structure of the periplasmic domain of the thermotoga maritima yidc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y82
- Type
- protein
- Length
- 796 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane protein insertase yidc
- UniProt
- Q9X1H2
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, B, C | Membrane protein insertase yidc | protein | 199 | 9% helix, 46% strand | Q9X1H2 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.58 | 0.75 | 46 | empty |
| 2 | 291 | 0.50 | 0.73 | 35 | empty |
| 3 | 52 | 0.42 | 0.82 | 11 | empty |
| 4 | 193 | 0.42 | 0.72 | 22 | empty |
| 5 | 78 | 0.36 | 0.77 | 22 | empty |
Interfaces
4 interfaces between chains.
- D–C · 168 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 136 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 134 Ų buried · 2 hydrogen bonds · protein-protein
- D–B · 117 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5Y82 · Crystal structure of the periplasmic domain of the Thermotoga maritima YidC · the same entry in another collection · chain D against D, TM-score 1.00
- Q9X1H2 · AlphaFold monomer V2.0 prediction for membrane protein insertase yidc (Q9X1H2) · a predicted model of the same protein · chain D 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 Q9X1H2
- Elsewhere: RCSB PDB 5Y82 · PDBe 5Y82 · UniProt Q9X1H2
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