2IBI: Covalent Ubiquitin-USP2 Complex

Covalent Ubiquitin-USP2 Complex. Determined by X-ray diffraction at 2.2 Å resolution. Released 24 Oct 2006.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,422
Mol. weight: 51.34 kDa
Ligands: ZN, NEH
Released: 24 Oct 2006

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

Secondary structure: helices and β-sheets

2IBI contains 20 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: 17 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	268-269	2	1
α-helix	276-286	11
α-helix	289-296	8
α-helix	300-303	4
α-helix	305-306	2
α-helix	312-326	15
β-strand	333-334	2	1
α-helix	337-346	10
α-helix	348-350	3
α-helix	358-372	15
α-helix	392-404	13
α-helix	410-415	6
β-strand	417-425	9	2
β-strand	431-438	8	2
β-strand	441-443	3	3
α-helix	444-446	3
β-strand	453-454	2	4
α-helix	455-462	8
β-strand	466-468	3	2
α-helix	470-472	3
α-helix	474	1
β-strand	475-476	2	5
β-strand	481-482	2	5
β-strand	485-493	9	2
β-strand	497-502	6	3
β-strand	505	1	6
β-strand	514	1	6
β-strand	519-520	2	4
β-strand	526-527	2	3
α-helix	529-531	3
β-strand	532	1	2
β-strand	540-552	13	3
β-strand	555-563	9	3
α-helix	564	1
β-strand	570-574	5	3
β-strand	577-581	5	3
α-helix	583-585	3
β-strand	591-598	8	3

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	7
β-strand	12-16	5	7
β-strand	22	1	8
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	7
β-strand	48-49	2	7
α-helix	50-51	2
β-strand	55	1	8
β-strand	66-70	5	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 2	A	protein	374	Homo sapiens	O75604 (AlphaFold model)
Ubiquitin	B	protein	75	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2IBI_1 Ubiquitin carboxyl-terminal hydrolase 2 (chains A)
MGSSHHHHHHSSGLVPRGSSSPGRDGMNSKSAQGLAGLRNLGNTCFMNSILQCLSNTREL
RDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFV
GYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRI
GDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGD
AAPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREF
ASENTNHAVYNLYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDA
YLLFYELASPPSRM

Sequence of entity 2 (B), FASTA

>2IBI_2 Ubiquitin (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
NEH	Ethanamine	C2 H7 N	1

Primary citation

Covalent Ubiquitin-USP2 Complex. Avvakumov, G.V., Walker, J.R., Bernstein, G. et al. To be published.

Other PDB entries of the same protein (UniProt O75604 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5XVE 1.24 Å, Crystal structure of human USP2 C276S mutant in complex with ubiquitin
3NHE 1.26 Å, High Resolution Structure (1.26A) of USP2a in Complex with Ubiquitin
3V6C 1.7 Å, Crystal Structure of USP2 in complex with mutated ubiquitin
5XU8 1.81 Å, Crystal structure of human USP2 in complex with ubiquitin and 6-thioguanine
2HD5 1.85 Å, USP2 in complex with ubiquitin
3V6E 2.1 Å, Crystal Structure of USP2 and a mutant form of Ubiquitin
6DGF 2.34 Å, Ubiquitin Variant bound to USP2

Browse structure collections

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