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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: 5BTF
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: GFN, MG
Pockets: 16 · 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	44% helix, 16% strand	P9WG45
D	DNA gyrase subunit B (EC 5.99.1.3)	protein	247	43% 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

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

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

Pockets

16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1086	0.86	0.87	138	MG, GFN
2	334	0.80	0.91	52	empty
3	302	0.77	0.89	43	empty
4	359	0.75	0.86	58	GFN
5	595	0.75	0.82	63	empty

Interfaces

27 interfaces between chains.

E–G · 2428 Å² buried · 773 hydrogen bonds · nucleic-nucleic
F–H · 2400 Å² buried · 788 hydrogen bonds · nucleic-nucleic
A–C · 1750 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1614 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1598 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

5BTF · 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 5BTF · PDBe 5BTF · UniProt P9WG47 · UniProt P9WG45

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