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Structure of mitoxantrone-bound ABCG2

Analyse Structure of mitoxantrone-bound ABCG2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7NFD
Type: protein
Length: 1,582 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-binding cassette sub-family G member 2; 5D3(FAB) light chain variable domain…
EC: 7.6.2.2
UniProt: Q9UNQ0
Ligands: MIX, NAG
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 3 distinct chains · 36% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	ATP-binding cassette sub-family G member 2 (EC 7.6.2.2)	protein	566	50% helix, 6% strand	Q9UNQ0
C, E	5D3(FAB) light chain variable domain	protein	107	3% helix, 29% strand	—
D, F	5D3(FAB) heavy chain variable domain	protein	118	3% helix, 21% strand	—

Ligands and binding sites

MIX · 1,4-dihydroxy-5,8-bis({2-[(2-hydroxyethyl) amino]ethyl}amino)-9,10-anthracenedione · 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

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	379	0.85	0.93	36	empty
2	902	0.79	0.81	80	MIX
3	597	0.71	0.79	65	empty
4	600	0.71	0.79	67	empty
5	506	0.70	0.80	49	empty

Interfaces

11 interfaces between chains.

A–B · 2312 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 772 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 761 Å² buried · 6 hydrogen bonds · protein-protein
C–B · 426 Å² buried · 4 hydrogen bonds · protein-protein
A–E · 425 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

7NFD · Structure of mitoxantrone-bound ABCG2 · the same entry in another collection · chain B against B, 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 0.89

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 7NFD · PDBe 7NFD · UniProt Q9UNQ0

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