Research workbench
Crystal structure of human ceramide-1-phosphate transfer protein (cptp) in complex with 12:0 ceramide-1-phosphate (12:0-C1P)
Analyse Crystal structure of human ceramide-1-phosphate transfer protein (cptp) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K85
- Type
- protein
- Length
- 830 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycolipid transfer protein domain-containing protein 1
- UniProt
- Q5TA50
- Ligands
- 1PZ
- Pockets
- 7 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glycolipid transfer protein domain-containing protein 1 | protein | 208 | 71% helix, 2% strand | Q5TA50 |
| B, D | Glycolipid transfer protein domain-containing protein 1 | protein | 207 | 71% helix, 2% strand | Q5TA50 |
Ligands and binding sites
- 1PZ · (2S,3R,4E)-2-(dodecanoylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.88 | 0.88 | 97 | 1PZ |
| 2 | 389 | 0.83 | 0.91 | 37 | 1PZ |
| 3 | 309 | 0.82 | 0.91 | 35 | 1PZ |
| 4 | 391 | 0.68 | 0.80 | 43 | empty |
| 5 | 236 | 0.56 | 0.78 | 33 | empty |
Interfaces
6 interfaces between chains.
- A–C · 436 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 378 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 368 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 288 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 223 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4K85 · Crystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5TA50 · AlphaFold monomer V2.0 prediction for ceramide-1-phosphate transfer protein (Q5TA50) · 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 Q5TA50
- Elsewhere: RCSB PDB 4K85 · PDBe 4K85 · UniProt Q5TA50
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