9DEK: USP7

USP7 in complex with macrocycle inhibitor MC02. Determined by X-ray diffraction at 2.0 Å resolution. Released 5 Mar 2025.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, synthetic construct
Chains: 4
Atoms: 6,155
Mol. weight: 88.87 kDa
Released: 5 Mar 2025

Explore 9DEK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DEK contains 42 α-helices and 43 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: 19 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	216	1	1
α-helix	225-233	9
α-helix	236-244	9
α-helix	252-254	3
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	288-292	5
α-helix	296-310	15
α-helix	319-324	6
β-strand	326-334	9	2
β-strand	340	1	2
β-strand	343-347	5	2
β-strand	350-352	3	3
β-strand	359	1	4
α-helix	360-368	9
α-helix	369-370	2
β-strand	371-373	3	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	409-412	4	6
β-strand	417-420	4	6
β-strand	426	1	4
β-strand	430-432	3	3
α-helix	434-436	3
β-strand	437	1	2
β-strand	447-459	13	3
β-strand	462-469	8	3
β-strand	478-481	4	3
β-strand	484-487	4	3
α-helix	490-493	4
α-helix	495-497	3
β-strand	511-520	10	3
α-helix	524-527	4
α-helix	533-535	3
α-helix	538-552	15

Chain B: 21 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	252-254	3
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	296-311	16
α-helix	319-324	6
β-strand	326-334	9	8
β-strand	340-347	8	8
β-strand	350-352	3	9
β-strand	359	1	10
α-helix	360-368	9
α-helix	370	1
β-strand	371-373	3	8
β-strand	379-380	2	11
α-helix	382-384	3
β-strand	386-387	2	11
β-strand	389-395	7	8
β-strand	401-406	6	9
β-strand	409-412	4	12
α-helix	413-415	3
β-strand	417-420	4	12
β-strand	426	1	10
β-strand	430-432	3	9
α-helix	434-436	3
β-strand	437	1	8
β-strand	447-459	13	9
β-strand	462-469	8	9
β-strand	478-481	4	9
β-strand	484-487	4	9
α-helix	490-493	4
α-helix	495-497	3
β-strand	511-520	10	9
α-helix	521-523	3
α-helix	524-527	4
α-helix	533-535	3
α-helix	538-547	10

Chains C and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 7	A, B	protein	368	Homo sapiens	Q93009 (AlphaFold model)
Macrocycle peptide MC02	C, D	protein	16	synthetic construct

Sequence of entity 1 (A, B), FASTA

>9DEK_1 Ubiquitin carboxyl-terminal hydrolase 7 (chains A, B)
MGSSHHHHHHSSGLVPRGSHMKKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMP
TEGDDSSKSVPLALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDN
VENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVD
YVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFE
FPEQLPLDEFLQKTDPKDPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVS
RCTKEEAIEHNYGGHDDDLSVRHCTNAYMLVYIRESKLSEVLQAVTDHDIPQQLVERLQE
EKRIEAQK

Sequence of entity 2 (C, D), FASTA

>9DEK_2 Macrocycle peptide  MC02 (chains C, D)
XFVTXGYLXVSXRRCG

Primary citation

Discovery and characterization of potent macrocycle inhibitors of ubiquitin-specific protease-7. Miranda, R., Anson, F., Smith, S.T. et al. Structure (2025) 33:705-717.e4. DOI 10.1016/j.str.2025.01.021 · 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…

Browse structure collections

About this viewer

MolViewer shows 9DEK directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.