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Cryo-EM structure of the ABCG2 E211Q mutant bound to estrone 3-sulfate and 5D3-Fab
Analyse Cryo-EM structure of the ABCG2 E211Q mutant bound to estrone 3-sulfate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HCO
- Type
- protein
- Length
- 1,576 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.58
- Source
- Homo sapiens; Mus musculus
- Molecule
- ATP-binding cassette sub-family G member 2; 5D3-Fab light chain; 5D3-Fab heavy chain
- UniProt
- Q9UNQ0
- Ligands
- FY5, NAG
- Pockets
- 18 · best druggability 0.85
Structure
electron microscopy · resolution 3.58 · 3 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ATP-binding cassette sub-family G member 2 | protein | 563 | 52% helix, 9% strand | Q9UNQ0 |
| C, E | 5D3-Fab light chain | protein | 107 | 3% helix, 36% strand | — |
| D, F | 5D3-Fab heavy chain | protein | 118 | 3% helix, 44% strand | — |
Ligands and binding sites
- FY5 · estrone 3-sulfate · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, D, F, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.85 | 0.95 | 34 | empty |
| 2 | 975 | 0.77 | 0.79 | 75 | FY5 |
| 3 | 684 | 0.76 | 0.82 | 75 | empty |
| 4 | 381 | 0.71 | 0.83 | 37 | empty |
| 5 | 398 | 0.70 | 0.82 | 36 | empty |
Interfaces
11 interfaces between chains.
- A–B · 2241 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 779 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 778 Ų buried · 9 hydrogen bonds · protein-protein
- C–B · 467 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 458 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6HCO · Cryo-EM structure of the ABCG2 E211Q mutant bound to estrone 3-sulfate and 5D3-Fab · the same entry in another collection · chain F against F, TM-score 1.00
- Q9UNQ0 · AlphaFold monomer V2.0 prediction for broad substrate specificity ATP-binding cassette… · a predicted model of the same protein · chain A against A, TM-score 0.88
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 Q9UNQ0
- Elsewhere: RCSB PDB 6HCO · PDBe 6HCO · UniProt Q9UNQ0
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