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Structure of topotecan-bound ABCG2

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

PDB: 7NEZ
Type: protein
Length: 1,576 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: TTC, NAG
Pockets: 18 · best druggability 0.85

Structure

electron microscopy · 3 distinct chains · 37% helix, 18% 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	563	51% helix, 9% strand	Q9UNQ0
C, E	5D3(FAB) light chain variable domain	protein	107	3% helix, 36% strand	—
D, F	5D3(FAB) heavy chain variable domain	protein	118	3% helix, 46% strand	—

Ligands and binding sites

TTC · (S)-10-[(dimethylamino)methyl]-4-ethyl-4,9-dihydroxy-1H-pyrano[3',4':6,7]inolizino[1,2-B]-quinoline-3, 14(4H,12H)-dione · ligand · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, D, B, F

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	361	0.85	0.94	34	empty
2	1068	0.77	0.79	79	TTC
3	652	0.77	0.82	85	empty
4	377	0.71	0.83	36	empty
5	394	0.70	0.82	36	empty

Interfaces

11 interfaces between chains.

A–B · 2236 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 766 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 756 Å² buried · 6 hydrogen bonds · protein-protein
A–E · 408 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 393 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

7NEZ · Structure of topotecan-bound ABCG2 · 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 7NEZ · PDBe 7NEZ · UniProt Q9UNQ0

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