MolNFT v1 · #97373 · protein
Crystal structure of human ceramide-1-phosphate transfer protein (cptp) in complex with 12:0 phosphatidic acid (12:0 pa)
4KBS · Glycolipid transfer protein domain-containing protein 1: “Crystal structure of human ceramide-1-phosphate transfer protein (cptp) in complex with 12:0 phosphatidic…”. X-ray diffraction, 1 ligand (PX2), 4 pockets (best druggability…
- PDB
- 4KBS
- Type
- protein
- Length
- 416 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycolipid transfer protein domain-containing protein 1
- UniProt
- Q5TA50
- Ligands
- PX2
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 69% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycolipid transfer protein domain-containing protein 1 | protein | 208 | 69% helix, 2% strand | Q5TA50 |
Ligands and binding sites
- PX2 · 1,2-dilauroyl-sn-glycero-3-phosphate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.87 | 0.88 | 87 | PX2, EDO |
| 2 | 124 | 0.39 | 0.74 | 17 | empty |
| 3 | 115 | 0.37 | 0.74 | 23 | empty |
| 4 | 89 | 0.35 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 775 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4KBS · 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 A against A, TM-score 0.96
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 4KBS · PDBe 4KBS · UniProt Q5TA50
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