2GFO: Ubiquitin carboxyl-terminal hydrolase 8

Name: PDB 2GFO: Structure of the Catalytic Domain of Human Ubiquitin Carboxyl-terminal Hydrolase 8
Published: 2006-04-04
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: hydrolase

Structure of the Catalytic Domain of Human Ubiquitin Carboxyl-terminal Hydrolase 8. Determined by X-ray diffraction at 2.0 Å resolution. Released 4 Apr 2006.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,938
Mol. weight: 45.72 kDa
Ligands: ZN
Released: 4 Apr 2006

Explore 2GFO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2GFO contains 14 α-helices and 23 β-strands across 1 chain. 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: 14 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	763-765	3
β-strand	768-769	2	1
β-strand	778-779	2	1
α-helix	786-796	11
α-helix	799-806	8
α-helix	810-813	4
α-helix	825-839	15
β-strand	842-845	4	1
α-helix	848-857	10
α-helix	859-861	3
α-helix	869-884	16
α-helix	903-917	15
α-helix	921-926	6
β-strand	928-936	9	2
β-strand	942-949	8	2
β-strand	952-954	3	3
α-helix	955-956	2
β-strand	961-963	3	4
α-helix	964-971	8
β-strand	975-977	3	2
β-strand	983-985	3	5
β-strand	990-992	3	5
β-strand	994-1002	9	2
β-strand	1006-1011	6	3
β-strand	1014-1016	3	6
β-strand	1021-1023	3	6
β-strand	1027-1029	3	4
β-strand	1035	1	7
α-helix	1038-1040	3
β-strand	1041	1	2
β-strand	1051	1	7
β-strand	1052-1060	9	3
β-strand	1067-1074	8	3
β-strand	1079-1084	6	3
β-strand	1087-1090	4	3
α-helix	1093-1096	4
β-strand	1101-1107	7	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 8	A	protein	396	Homo sapiens	P40818 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2GFO_1 Ubiquitin carboxyl-terminal hydrolase 8 (chains A)
MGSSHHHHHHSSGLVPRGSPTVTPTVNRENKPTCYPKAEISRLSASQIRNLNPVFGGSGP
ALTGLRNLGNTCYMNSILQCLCNAPHLADYFNRNCYQDDINRSNLLGHKGEVAEEFGIIM
KALWTGQYRYISPKDFKITIGKINDQFAGYSQQDSQELLLFLMDGLHEDLNKADNRKRYK
EENNDHLDDFKAAEHAWQKHKQLNESIIVALFQGQFKSTVQCLTCHKKSRTFEAFMYLSL
PLASTSKCTLQDCLRLFSKEEKLTDNNRFYCSHCRARRDSLKKIEIWKLPPVLLVHLKRF
SYDGRWKQKLQTSVDFPLENLDLSQYVIGPKNNLKKYNLFSVSNHYGGLDGGHYTAYCKN
AARQRWFKFDDHEVSDISVSSVKSSAAYILFYTSLG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Amino-terminal Dimerization, NRDP1-Rhodanese Interaction, and Inhibited Catalytic Domain Conformation of the Ubiquitin-specific Protease 8 (USP8). Avvakumov, G.V., Walker, J.R., Xue, S. et al. J Biol Chem (2006) 281:38061-38070. DOI 10.1074/jbc.M606704200 · PubMed

Other PDB entries of the same protein (UniProt P40818 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6F09 1.59 Å, Binary complex of 14-3-3 zeta with ubiquitin specific protease 8 (USP8) pSer718 peptide
8ADM 1.7 Å, Ternary complex of 14-3-3 sigma, Usp8pS718 phosphopeptide and small molecule stabilizer
2A9U 2.1 Å, Structure of the N-terminal domain of Human Ubiquitin carboxyl-terminal hydrolase 8 (USP8)
8XPN 2.1 Å, The Crystal Structure of USP8 from Biortus.
2GWF 2.3 Å, Structure of a USP8-NRDP1 complex
3N3K 2.6 Å, The catalytic domain of USP8 in complex with a USP8 specific inhibitor
8Y9A 3.1 Å, The Crystal Structure of USP8 from Biortus.
1WHB Solution structure of the Rhodanese-like domain in human ubiquitin specific protease 8…

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