MolNFT v1 · #36116 · protein
Crystal structure of human glycolipid transfer protein complexed with N-hexyl-beta-D-glucoside
2EVS: “Crystal structure of human glycolipid transfer protein complexed with N-hexyl-beta-D-glucoside”. X-ray diffraction, 2 ligands (D10, GLC), 3 pockets (best druggability 0.77). MolNFT v1 #36116 on GenesisL1: 3D structure, binding sites…
- PDB
- 2EVS
- Type
- protein
- Length
- 393 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycolipid transfer protein
- UniProt
- Q9NZD2
- Ligands
- D10, GLC
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycolipid transfer protein | protein | 205 | 65% helix, 2% strand | Q9NZD2 |
| E | Glycolipid transfer protein | protein | 188 | 68% helix, 2% strand | Q9NZD2 |
Ligands and binding sites
- D10 · Decane · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, E
- HEX · Hexane · additive · 3 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.77 | 0.91 | 28 | D10 |
| 2 | 289 | 0.75 | 0.87 | 33 | HEX |
| 3 | 511 | 0.72 | 0.81 | 57 | GLC, HEX |
Interfaces
1 interface between chains.
- A–E · 677 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2EVS · 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 E 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 2EVS · PDBe 2EVS · UniProt Q9NZD2
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