Research workbench
Crystal structure of human glycolipid transfer protein complexed with 12:0 lactosylceramide
Analyse Crystal structure of human glycolipid transfer protein complexed with 12:0… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EVD
- Type
- protein
- Length
- 204 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycolipid transfer protein
- UniProt
- Q9NZD2
- Ligands
- SPH, DAO, D10, BGC, GAL
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycolipid transfer protein | protein | 204 | 68% helix, 2% strand | Q9NZD2 |
Ligands and binding sites
- SPH · Sphingosine · ligand · chains A
- DAO · Lauric acid · ligand · chains A
- D10 · Decane · ligand · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- OCT · N-octane · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.77 | 0.86 | 33 | SPH, DAO, D10 |
| 2 | 52 | 0.54 | 0.88 | 12 | empty |
Compared structures
- 2EVD · Crystal structure of human Glycolipid Transfer Protein complexed with 12:0… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NZD2 · AlphaFold monomer V2.0 prediction for glycolipid transfer protein (Q9NZD2) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9NZD2
- Elsewhere: RCSB PDB 2EVD · PDBe 2EVD · UniProt Q9NZD2
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