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Crystal structure of a topoisomerase II complex

Analyse Crystal structure of a topoisomerase II complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5BTA
Type: protein + DNA
Length: 1,546 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA gyrase subunit a; DNA gyrase subunit B; DNA substrate 24-mer…
EC: 5.99.1.3
UniProt: P9WG47, P9WG45
Ligands: MFX, MG
Pockets: 14 · best druggability 0.86

Structure

x-ray diffraction · 5 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	DNA gyrase subunit a (EC 5.99.1.3)	protein	487	50% helix, 17% strand	P9WG47
B	DNA gyrase subunit B (EC 5.99.1.3)	protein	245	45% helix, 16% strand	P9WG45
D	DNA gyrase subunit B (EC 5.99.1.3)	protein	247	45% helix, 15% strand	P9WG45
E, H	DNA substrate 24-mer ggtcatgaatgactatgcacgtaa	dna	20	—	—
F, G	DNA substrate 24-mer ttacgtgcatagtcattcatgacc	dna	20	—	—

Ligands and binding sites

MFX · 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid · ligand · 2 copies · chains A, C, D, E, F, G, H, B
MG · Magnesium ion · metal · 4 copies · chains A, E, G, B, C, F, H, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1101	0.86	0.87	142	MG, MFX
2	367	0.80	0.90	53	empty
3	497	0.77	0.85	70	empty
4	562	0.75	0.82	60	empty
5	257	0.75	0.89	45	MG, MFX

Interfaces

27 interfaces between chains.

F–H · 2436 Å² buried · 768 hydrogen bonds · nucleic-nucleic
E–G · 2429 Å² buried · 777 hydrogen bonds · nucleic-nucleic
A–C · 1792 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1621 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1620 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

5BTA · Crystal structure of a topoisomerase II complex · the same entry in another collection · chain H against H, TM-score 1.00
P9WG47 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (P9WG47) · a predicted model of the same protein · chain A against A, TM-score 0.98
P9WG45 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P9WG45) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 P9WG47
Every structure of UniProt P9WG45
Elsewhere: RCSB PDB 5BTA · PDBe 5BTA · UniProt P9WG47 · UniProt P9WG45

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