MolNFT v1 · #97266 · protein
Crystal structure of human ceramide-1-phosphate transfer protein (cptp) in complex with 18:1 ceramide-1-phosphate (18:1-C1P)
4K8N · Glycolipid transfer protein domain-containing protein 1: “Crystal structure of human ceramide-1-phosphate transfer protein (cptp) in complex with 18:1…”. X-ray diffraction, 1 ligand (1Q0), 11 pockets (best druggability 0.88). MolNFT…
- PDB
- 4K8N
- Type
- protein
- Length
- 1,237 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
- 1Q0
- Pockets
- 11 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Glycolipid transfer protein domain-containing protein 1 | protein | 207 | 67% helix, 2% strand | Q5TA50 |
| B, C, D | Glycolipid transfer protein domain-containing protein 1 | protein | 206 | 65% helix, 2% strand | Q5TA50 |
| F | Glycolipid transfer protein domain-containing protein 1 | protein | 205 | 65% helix, 2% strand | Q5TA50 |
Ligands and binding sites
- 1Q0 · (2S,3R,4Z)-3-hydroxy-2-[(9E)-octadec-9-enoylamino]octadec-4-en-1-yl dihydrogen phosphate · ligand · 6 copies · chains A, E, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.88 | 0.88 | 102 | 1Q0 |
| 2 | 476 | 0.86 | 0.91 | 47 | 1Q0 |
| 3 | 519 | 0.85 | 0.90 | 43 | 1Q0 |
| 4 | 510 | 0.81 | 0.86 | 45 | 1Q0 |
| 5 | 367 | 0.79 | 0.88 | 40 | 1Q0 |
Interfaces
6 interfaces between chains.
- D–F · 460 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 428 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 363 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 353 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 273 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4K8N · 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 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 4K8N · PDBe 4K8N · UniProt Q5TA50
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