5VSB: DUB complex

Structure of DUB complex. Determined by X-ray diffraction at 1.85 Å resolution. Released 20 Dec 2017.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,703
Mol. weight: 82.86 kDa
Ligands: 9QA
Released: 20 Dec 2017

Explore 5VSB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VSB contains 36 α-helices and 42 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: 19 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	216	1	1
α-helix	225-233	9
α-helix	236-243	8
α-helix	256-269	14
α-helix	273	1
β-strand	274	1	1
α-helix	275	1
α-helix	277-283	7
α-helix	288-293	6
α-helix	296-310	15
α-helix	319-324	6
β-strand	326-334	9	2
β-strand	340-347	8	2
β-strand	350-352	3	3
β-strand	359	1	4
α-helix	360-367	8
α-helix	369	1
β-strand	370-373	4	2
β-strand	379-380	2	5
α-helix	382-384	3
β-strand	386-387	2	5
β-strand	389-395	7	2
β-strand	401-406	6	3
β-strand	409-410	2	6
β-strand	419-420	2	6
β-strand	426	1	4
β-strand	430-432	3	3
α-helix	434-436	3
β-strand	437	1	2
β-strand	447-457	11	3
β-strand	464-469	6	3
β-strand	477-481	5	3
β-strand	484-488	5	3
α-helix	490-493	4
α-helix	495-497	3
β-strand	511-520	10	3
α-helix	521-523	3
α-helix	524-527	4
α-helix	533-535	3
α-helix	538-551	14

Chain B: 17 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	216	1	7
α-helix	225-233	9
α-helix	236-244	9
α-helix	256-269	14
α-helix	273	1
β-strand	274	1	7
α-helix	275	1
α-helix	277-283	7
α-helix	288-292	5
α-helix	296-310	15
α-helix	319-324	6
β-strand	326-334	9	2
β-strand	340-347	8	2
β-strand	350-352	3	8
β-strand	359	1	9
α-helix	360-368	9
α-helix	370	1
β-strand	371-373	3	2
β-strand	379	1	10
β-strand	387	1	10
β-strand	389-395	7	2
β-strand	401-406	6	8
β-strand	409-411	3	11
β-strand	418-420	3	11
β-strand	426	1	9
β-strand	430-432	3	8
β-strand	437	1	2
β-strand	447-458	12	8
β-strand	463-469	7	8
β-strand	478-481	4	8
β-strand	484-487	4	8
α-helix	490-493	4
α-helix	495-497	3
β-strand	512-520	9	8
α-helix	521-523	3
α-helix	524-527	4
α-helix	533-535	3
α-helix	538-547	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 7	A, B	protein	353	Homo sapiens	Q93009 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5VSB_1 Ubiquitin carboxyl-terminal hydrolase 7 (chains A, B)
KKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLALQRVFYEL
QHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVEGTIPKLFRGK
MVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGLQ
EAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPAN
YILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDDDLSV
RHCTNAYMLVYIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQKRKERQE

Ligands and cofactors

ID	Name	Formula	Copies
9QA	7-chloro-3-{[4-hydroxy-1-(3-phenylpropanoyl)piperidin-4-yl]methyl}quinazolin-4(…	C23 H24 Cl N3 O3	2

Primary citation

Structure-Guided Development of a Potent and Selective Non-covalent Active-Site Inhibitor of USP7. Lamberto, I., Liu, X., Seo, H.S. et al. Cell Chem Biol (2017) 24:1490-1500.e11. DOI 10.1016/j.chembiol.2017.09.003 · PubMed

Other PDB entries of the same protein (UniProt Q93009 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4YSI 1.02 Å, Structure of USP7 with a novel viral protein
5KYC 1.43 Å, Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin…
5KYF 1.45 Å, Crystal structure of USP7 catalytic domain [L299A] mutant in complex with ubiquitin
2FOJ 1.6 Å, The Crystal Structure of the N-terminal domain of HAUSP/USP7 complexed with p53 peptide…
2XXN 1.6 Å, Structure of the vIRF4-HAUSP TRAF domain complex
5KYD 1.62 Å, Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin
12ZJ 1.63 Å, Crystal structure of USP7 TRAF domain in complex with MAGEL2 peptide (968-980)
2F1W 1.65 Å, Crystal structure of the TRAF-like domain of HAUSP/USP7
1YY6 1.7 Å, The Crystal Structure of the N-terminal domain of HAUSP/USP7 complexed with an EBNA1…
2F1Y 1.7 Å, Crystal structure of the TRAF-like domain of HAUSP/USP7 bound to a MDM2 peptide
4KG9 1.7 Å, Crystal Structure Of USP7-NTD with MCM-BP
5N9T 1.73 Å, Crystal structure of USP7 in complex with a potent, selective and reversible…

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