5KYD: USP7 catalytic domain [V302K] mutant

Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin. Determined by X-ray diffraction at 1.62 Å resolution. Released 9 Aug 2017.

Method: X-ray diffraction
Resolution: 1.62 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,792
Mol. weight: 49.19 kDa
Released: 9 Aug 2017

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

Secondary structure: helices and β-sheets

5KYD contains 22 α-helices and 28 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	3
α-helix	225-233	9
α-helix	236-243	8
α-helix	256-269	14
α-helix	273	1
β-strand	274	1	3
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	4
β-strand	340-347	8	4
β-strand	350-352	3	5
β-strand	359	1	6
α-helix	360-367	8
β-strand	371-373	3	4
α-helix	375-377	3
β-strand	379-380	2	7
α-helix	382-384	3
β-strand	386-387	2	7
β-strand	389-397	9	4
β-strand	401-406	6	5
β-strand	409-412	4	8
β-strand	417-420	4	8
β-strand	426	1	6
β-strand	430-432	3	5
α-helix	434-436	3
β-strand	437	1	4
β-strand	447-458	12	5
β-strand	463-469	7	5
β-strand	477-481	5	5
β-strand	484-488	5	5
α-helix	490-493	4
α-helix	495-497	3
β-strand	511-520	10	5
α-helix	521-523	3
α-helix	524-527	4
α-helix	533-535	3
α-helix	538-547	10

Chain D: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	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
β-strand	55	1	2
α-helix	56-59	4
β-strand	66-71	6	1

Molecules and chains

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

Sequence of entity 1 (D), FASTA

>5KYD_1 Polyubiquitin-B (chains D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 2 (A), FASTA

>5KYD_2 Ubiquitin carboxyl-terminal hydrolase 7 (chains A)
GSHMKKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLALQRV
FYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRKLLDNVENKMKGTCVEGTIPKL
FRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGE
HGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPK
DPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDD
DLSVRHCTNAYMLVYIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQK

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 P0CG47 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NVG 1.07 Å, Thr12 Phosphorylated Ubiquitin
5TOG 1.08 Å, Room temperature structure of ubiquitin variant u7ub25.2540
5TOF 1.12 Å, Room temperature structure of ubiquitin variant u7ub25
4XOF 1.15 Å, Observing the overall rocking motion of a protein in a crystal - Orthorhombic Ubiquitin…
5GOD 1.15 Å, Lys27-linked di-ubiquitin
5GOB 1.15 Å, Lys6-linked di-ubiquitin
5W46 1.18 Å, Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution
7S6O 1.25 Å, The crystal structure of Lys48-linked di-ubiquitin
8IC9 1.25 Å, Lys48-linked K48C-diubiquitin
5DK8 1.32 Å, Human ubiquitin in the P1 space group
7CAP 1.33 Å, Cyclic Lys48-linked triubiquitin
5V1Y 1.42 Å, Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex

Browse structure collections

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