7XHH: Ubiquitin carboxyl-terminal hydrolase 7

Name: PDB 7XHH: High-resolution X-ray cocrystal structure of USP7 in complex with X4
Published: 2023-04-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: hydrolase

High-resolution X-ray cocrystal structure of USP7 in complex with X4. Determined by X-ray diffraction at 2.1 Å resolution. Released 19 Apr 2023.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,788
Mol. weight: 81.65 kDa
Ligands: DYO
Released: 19 Apr 2023

Explore 7XHH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7XHH contains 41 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: 21 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	208-210	3
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	288-292	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	3
α-helix	353	1
β-strand	359	1	4
α-helix	360-367	8
β-strand	371-373	3	2
α-helix	375-377	3
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	447-457	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	538-552	15

Chain B: 20 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	216	1	7
α-helix	225-233	9
α-helix	236-243	8
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	8
β-strand	340-347	8	8
β-strand	350-352	3	9
β-strand	359	1	10
α-helix	360-368	9
β-strand	371-373	3	8
α-helix	375-377	3
β-strand	379-380	2	11
α-helix	382-384	3
β-strand	386-387	2	11
β-strand	389-397	9	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	447-457	11	9
β-strand	464-469	6	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	538-552	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 7	A, B	protein	348	Homo sapiens	Q93009 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7XHH_1 Ubiquitin carboxyl-terminal hydrolase 7 (chains A, B)
SKKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLALQRVFYE
LQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVEGTIPKLFRG
KMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGL
QEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPA
NYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDDDLS
VRHCTNAYMLVYIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQK

Ligands and cofactors

ID	Name	Formula	Copies
DYO	3-[4-(aminomethyl)phenyl]-6-[[1-[[2-chloranyl-4-(1,2,4-oxadiazol-3-yl)phenyl]me…	C28 H29 Cl N8 O3	2

Primary citation

High-resolution X-ray cocrystal structure of USP7 in complex with X4. Wen, X.A. To be published.

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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