5KYF: USP7 catalytic domain [L299A] mutant

Crystal structure of USP7 catalytic domain [L299A] mutant in complex with ubiquitin. Determined by X-ray diffraction at 1.45 Å resolution. Released 9 Aug 2017.

Method: X-ray diffraction
Resolution: 1.45 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,888
Mol. weight: 49.31 kDa
Released: 9 Aug 2017

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

Secondary structure: helices and β-sheets

5KYF contains 23 α-helices and 30 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 B: 19 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	216	1	1
α-helix	223-233	11
α-helix	236-244	9
α-helix	256-269	14
α-helix	273	1
β-strand	274	1	1
α-helix	275	1
α-helix	277-283	7
β-strand	287	1	2
β-strand	291	1	2
α-helix	296-311	16
α-helix	319-324	6
β-strand	326-334	9	3
β-strand	340-347	8	3
β-strand	350-352	3	4
β-strand	359	1	5
α-helix	360-367	8
β-strand	371-373	3	3
α-helix	375-377	3
β-strand	379-380	2	6
α-helix	382-384	3
β-strand	386-387	2	6
β-strand	389-397	9	3
β-strand	401-406	6	4
β-strand	409-412	4	7
β-strand	417-420	4	7
β-strand	426	1	5
β-strand	430-432	3	4
α-helix	434-436	3
β-strand	437	1	3
β-strand	447-459	13	4
β-strand	462-469	8	4
β-strand	477-481	5	4
β-strand	484-488	5	4
α-helix	490-493	4
α-helix	495-497	3
α-helix	508-510	3
β-strand	511-520	10	4
α-helix	521-523	3
α-helix	524-527	4
α-helix	533-535	3
α-helix	538-550	13

Chain C: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	8
β-strand	12-16	5	8
β-strand	22	1	9
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	8
β-strand	48-49	2	8
α-helix	50	1
β-strand	55	1	9
α-helix	57-59	3
β-strand	66-70	5	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 7	B	protein	351	Homo sapiens	Q93009 (AlphaFold model)
Polyubiquitin-B	C	protein	76	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>5KYF_1 Ubiquitin carboxyl-terminal hydrolase 7 (chains B)
GSHMKKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLALQRV
FYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQEACRVLLDNVENKMKGTCVEGTIPKL
FRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGE
HGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPK
DPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDD
DLSVRHCTNAYMLVYIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQK

Sequence of entity 2 (C), FASTA

>5KYF_2 Polyubiquitin-B (chains C)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Primary citation

Selectively Modulating Conformational States of USP7 Catalytic Domain for Activation. Ozen, A., Rouge, L., Bashore, C. et al. Structure (2018) 26:72-84.e7. DOI 10.1016/j.str.2017.11.010 · 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…
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…
9DEM 1.77 Å, USP7 in complex with macrocycle MC04

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