Research workbench
Crystal structure of the ceramide transfer protein pH and start domain complex
Analyse Crystal structure of the ceramide transfer protein pH and start domain complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JJD
- Type
- protein
- Length
- 331 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagen type IV alpha-3-binding protein
- UniProt
- Q9Y5P4
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagen type IV alpha-3-binding protein | protein | 97 | 25% helix, 43% strand | Q9Y5P4 |
| B | Collagen type IV alpha-3-binding protein | protein | 234 | 26% helix, 38% strand | Q9Y5P4 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, A
- PGE · Triethylene 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.83 | 0.88 | 52 | PEG, PGE |
| 2 | 383 | 0.66 | 0.80 | 51 | PEG |
| 3 | 84 | 0.32 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 665 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5JJD · crystal structure of the ceramide transfer protein PH and START domain complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y5P4 · AlphaFold monomer V2.0 prediction for ceramide transfer protein (Q9Y5P4) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q9Y5P4
- Elsewhere: RCSB PDB 5JJD · PDBe 5JJD · UniProt Q9Y5P4
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