6Q00: TDP2 UBA Domain

TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 1. Determined by X-ray diffraction at 0.85 Å resolution. Released 29 Apr 2020.

Method: X-ray diffraction
Resolution: 0.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,557
Mol. weight: 13.7 kDa
Released: 29 Apr 2020

Explore 6Q00 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Q00 contains 8 α-helices and 7 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
β-strand	55	1	2
α-helix	57-59	3
β-strand	66-71	6	1
α-helix	72	1

Chain B: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	23-36	14
α-helix	40-49	10
α-helix	54-62	9
α-helix	64-65	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	A	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
Tyrosyl-DNA phosphodiesterase 2	B	protein	45	Homo sapiens	O95551 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6Q00_1 Ubiquitin (chains A)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 2 (B), FASTA

>6Q00_2 Tyrosyl-DNA phosphodiesterase 2 (chains B)
SNARRLLCVEFASVASCDAAVAQCFLAENDWEMERALNSYFEPPV

Primary citation

Ubiquitin stimulated reversal of topoisomerase 2 DNA-protein crosslinks by TDP2. Schellenberg, M.J., Appel, C.D., Riccio, A.A. et al. Nucleic Acids Res (2020) 48:6310-6325. DOI 10.1093/nar/gkaa318 · PubMed

Other PDB entries of the same protein (UniProt P0CG48 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1OGW 1.32 Å, Synthetic Ubiquitin with fluoro-Leu at 50 and 67
5NL4 1.32 Å, Crystal structure of Zn1.3-E16V human ubiquitin (hUb) mutant adduct, from a solution 35…
2GBJ 1.35 Å, Crystal Structure of the 9-10 8 Glycine Insertion Mutant of Ubiquitin.
4HK2 1.4 Å, U7Ub25.2540
9FJ3 1.4 Å, Structure of ubiquitin bound of coiled-coil UIM form 2
1XD3 1.45 Å, Crystal structure of UCHL3-UbVME complex
4IUM 1.45 Å, Equine arteritis virus papain-like protease 2 (PLP2) covalently bound to ubiquitin
7UV5 1.45 Å, The crystal structure of Papain-Like Protease of SARS CoV-2, C111S/D286N mutant, in…
5NLF 1.5 Å, Crystal structure of Zn2.7-E16V human ubiquitin (hUb) mutant adduct, from a solution 100…
9F6G 1.5 Å, Human USP30 chimera bound to Ubiquitin-PA
9OVX 1.5 Å, Crystal structure of ubiquitin K27M mutant
4UN2 1.51 Å, Crystal structure of the UBA domain of Dsk2 in complex with Ubiquitin

Browse structure collections

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