MolNFT v1 · #78129 · protein
Crystal structure of human glycolipid transfer protein complexed with 3-O-sulfo-galactosylceramide containing nervonoyl acyl chain (24:1)
3RZN: “Crystal structure of human glycolipid transfer protein complexed with 3-O-sulfo-galactosylceramide containing…”. X-ray diffraction, 1 ligand (CIS), 2 pockets (best druggability 0.77). MolNFT v1 #78129 on GenesisL1: 3D structure…
- PDB
- 3RZN
- Type
- protein
- Length
- 206 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycolipid transfer protein
- UniProt
- Q9NZD2
- Ligands
- CIS
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 67% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycolipid transfer protein | protein | 206 | 67% helix, 1% strand | Q9NZD2 |
Ligands and binding sites
- CIS · (15Z)-N-((1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-enyl)tetracos-15-enamide · ligand · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.77 | 0.85 | 36 | CIS |
| 2 | 77 | 0.41 | 0.79 | 21 | empty |
Compared structures
- 3RZN · Crystal Structure of Human Glycolipid Transfer Protein complexed with… · 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 0.97
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 3RZN · PDBe 3RZN · UniProt Q9NZD2
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