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Crystal structure of human gltp bound with 12:0 monosulfatide (orthorhombic form; four subunits in asymmetric unit)
Analyse Crystal structure of human gltp bound with 12:0 monosulfatide (orthorhombic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GXG
- Type
- protein
- Length
- 830 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycolipid transfer protein
- UniProt
- Q9NZD2
- Ligands
- EIS
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycolipid transfer protein | protein | 209 | 68% helix, 1% strand | Q9NZD2 |
| B | Glycolipid transfer protein | protein | 207 | 67% helix, 2% strand | Q9NZD2 |
| D | Glycolipid transfer protein | protein | 206 | 66% helix, 1% strand | Q9NZD2 |
| E | Glycolipid transfer protein | protein | 208 | 64% helix, 3% strand | Q9NZD2 |
Ligands and binding sites
- EIS · N-{(2S,3R,4E)-3-hydroxy-1-[(3-O-sulfo-beta-D-galactopyranosyl)oxy]octadec-4-en-2-yl}dodecanamide · ligand · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.84 | 0.85 | 71 | EIS |
| 2 | 799 | 0.82 | 0.84 | 56 | EIS |
| 3 | 382 | 0.61 | 0.77 | 47 | empty |
| 4 | 66 | 0.60 | 0.90 | 15 | empty |
| 5 | 53 | 0.53 | 0.88 | 13 | empty |
Interfaces
4 interfaces between chains.
- D–E · 514 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 511 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 285 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 230 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4GXG · Crystal structure of human GLTP bound with 12:0 monosulfatide (orthorhombic form; four… · the same entry in another collection · chain E against E, TM-score 1.00
- Q9NZD2 · AlphaFold monomer V2.0 prediction for glycolipid transfer protein (Q9NZD2) · a predicted model of the same protein · chain B 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 4GXG · PDBe 4GXG · UniProt Q9NZD2
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