Research workbench
Crystal structure of cert start domain in complex with compound E16A
Analyse Crystal structure of cert start domain in complex with compound E16A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZYJ
- Type
- protein
- Length
- 228 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipid-transfer protein cert
- UniProt
- Q9Y5P4
- Ligands
- 9ML
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipid-transfer protein cert | protein | 228 | 27% helix, 39% strand | Q9Y5P4 |
Ligands and binding sites
- 9ML · 2-[4-[4-pentyl-3-[(1~{S},2~{R})-2-pyridin-2-ylcyclopropyl]phenyl]phenyl]sulfonylethanol · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.85 | 0.91 | 51 | 9ML |
| 2 | 96 | 0.35 | 0.74 | 19 | empty |
| 3 | 66 | 0.31 | 0.75 | 19 | GOL |
Compared structures
- 5ZYJ · Crystal structure of CERT START domain in complex with compound E16A · 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 A 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 Q9Y5P4
- Elsewhere: RCSB PDB 5ZYJ · PDBe 5ZYJ · UniProt Q9Y5P4
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