6Q01: TDP2 UBA Domain

TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2. Determined by X-ray diffraction at 0.85 Å resolution. Released 29 Apr 2020.

Method: X-ray diffraction
Resolution: 0.85 Å
Organisms: Bos taurus, Homo sapiens
Chains: 4
Atoms: 3,162
Mol. weight: 27.56 kDa
Ligands: MG, BEZ
Released: 29 Apr 2020

Explore 6Q01 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6Q01 contains 14 α-helices and 16 β-strands across 4 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
α-helix	50-51	2
β-strand	55	1	2
α-helix	57-59	3
β-strand	66-71	6	1

Chain B: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	3
β-strand	12-16	5	3
β-strand	22	1	4
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	3
β-strand	48-49	2	3
α-helix	50-51	2
β-strand	52	1	5
β-strand	54	1	5
β-strand	55	1	4
α-helix	57-59	3
β-strand	66-71	6	3

Chains C and D: 3 helices, 0 β-strands

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	A, B	protein	76	Bos taurus	P62992 (AlphaFold model)
Tyrosyl-DNA phosphodiesterase 2	C, D	protein	45	Homo sapiens	O95551 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6Q01_1 Ubiquitin (chains A, B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 2 (C, D), FASTA

>6Q01_2 Tyrosyl-DNA phosphodiesterase 2 (chains C, D)
SNARRLLCVEFASVASCDAAVAQCFLAENDWEMERALNSYFEPPV

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
BEZ	Benzoic acid	C7 H6 O2	1

Water and common crystallization additives (EDO, K) are not listed.

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 P62992 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5XVE 1.24 Å, Crystal structure of human USP2 C276S mutant in complex with ubiquitin
4M0W 1.4 Å, Crystal Structure of SARS-CoV papain-like protease C112S mutant in complex with ubiquitin
4Y1H 1.4 Å, Crystal structure of K33 linked tri-Ubiquitin
6E2B 1.45 Å, Ubiquitin in complex with Pt(2-phenilpyridine)(PPh3)
5XU8 1.81 Å, Crystal structure of human USP2 in complex with ubiquitin and 6-thioguanine
5MN9 2.05 Å, Crystal structure of MINDY-1 tMIU in complex with K48-diUb
5BZ0 2.1 Å, Crystal structure of IBV papain-like protease PLpro C101S mutant in complex with ubiquitin
7F0U 2.2 Å, porcine epidemic diarrhea virus papain-like protease 2 C44S mutant in complex with mono…
4Z9S 2.3 Å, Non-covalent assembly of monoubiquitin that mimics K11 poly-ubiquitin
5FER 2.34 Å, Complex of TRIM25 RING with UbcH5-Ub
5JQS 2.65 Å, Crystal structure of deubiquitinase MINDY-1 in complex with Ubiquitin
6DJW 3.8 Å, Crystal Structure of pParkin (REP and RING2 deleted)-pUb-UbcH7 complex

Browse structure collections

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