Research workbench
Crystal structure of human ceramide-1-phosphate transfer protein (cptp) in complex with 8:0 ceramide-1-phosphate (8:0-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
- 4KF6
- Type
- protein
- Length
- 1,238 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycolipid transfer protein domain-containing protein 1
- UniProt
- Q5TA50
- Ligands
- 1T9
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F | Glycolipid transfer protein domain-containing protein 1 | protein | 206 | 66% helix, 2% strand | Q5TA50 |
| B | Glycolipid transfer protein domain-containing protein 1 | protein | 208 | 63% helix, 2% strand | Q5TA50 |
Ligands and binding sites
- 1T9 · (2S,3R,4E)-3-hydroxy-2-(octanoylamino)octadec-4-en-1-yl dihydrogen phosphate · ligand · 6 copies · chains A, D, B, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.79 | 0.81 | 66 | 1T9 |
| 2 | 823 | 0.78 | 0.81 | 82 | 1T9 |
| 3 | 952 | 0.77 | 0.79 | 83 | 1T9 |
| 4 | 610 | 0.75 | 0.81 | 56 | 1T9 |
| 5 | 539 | 0.75 | 0.82 | 57 | 1T9 |
Interfaces
12 interfaces between chains.
- A–B · 403 Ų buried · 2 hydrogen bonds · protein-protein
- E–F · 379 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 367 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 355 Ų buried · 1 hydrogen bond · protein-protein
- D–E · 349 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4KF6 · Crystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with… · the same entry in another collection · chain F against F, 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 E 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 4KF6 · PDBe 4KF6 · UniProt Q5TA50
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