MolNFT v1 · #123422 · protein
Crystal structure of the ceramide transfer protein pH and start domain complex
5JJD · Collagen type IV alpha-3-binding protein: “Crystal structure of the ceramide transfer protein pH and start domain complex”. X-ray diffraction, 3 pockets (best druggability 0.83). MolNFT v1 #123422 on GenesisL1: 3D structure, binding…
- 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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