3H8V: Human Ubiquitin-activating Enzyme 5

Human Ubiquitin-activating Enzyme 5 in Complex with ATP. Determined by X-ray diffraction at 2.0 Å resolution. Released 26 May 2009.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,615
Mol. weight: 64.97 kDa
Ligands: ZN, ATP
Released: 26 May 2009

Explore 3H8V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3H8V contains 15 α-helices and 26 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: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	70-73	4
β-strand	75-79	5	1
α-helix	83-95	13
β-strand	99-103	5	1
β-strand	107	1	2
β-strand	123	1	3
β-strand	125	1	3
β-strand	126	1	2
α-helix	127-138	12
β-strand	143-147	5	1
α-helix	154-166	13
β-strand	167	1	4
β-strand	173	1	4
β-strand	177-180	4	1
α-helix	185-198	14
β-strand	202-207	6	1
β-strand	213-219	7	1
α-helix	232-233	2
α-helix	247-274	28
β-strand	282-286	5	1
β-strand	291	1	1
β-strand	294-295	2	1
α-helix	306-317	12

Chain B: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	71-73	3
β-strand	75-79	5	5
α-helix	84-95	12
β-strand	99-103	5	5
α-helix	127-138	12
β-strand	143-147	5	5
α-helix	154-166	13
β-strand	167	1	6
β-strand	173	1	6
β-strand	177-180	4	5
α-helix	185-198	14
β-strand	202-207	6	5
β-strand	213-219	7	5
α-helix	250-274	25
β-strand	282-286	5	5
β-strand	291	1	5
β-strand	294-295	2	5
α-helix	306-319	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like modifier-activating enzyme 5	A, B	protein	292	Homo sapiens	Q9GZZ9 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3H8V_1 Ubiquitin-like modifier-activating enzyme 5 (chains A, B)
MGSSHHHHHHSSGLVPRGSMALKRMGIVSDYEKIRTFAVAIVGVGGVGSVTAEMLTRCGI
GKLLLFDYDKVELANMNRLFFQPHQAGLSKVQAAEHTLRNINPDVLFEVHNYNITTVENF
QHFMDRISNGGLEEGKPVDLVLSCVDNFEARMTINTACNELGQTWMESGVSENAVSGHIQ
LIIPGESACFACAPPLVVAANIDEKTLKREGVCAASLPTTMGVVAGILVQNVLKFLLNFG
TVSFYLGYNAMQDFFPTMSMKPNPQCDDRNCRKQQEEYKKKVAALPKQEVIQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1

Primary citation

Crystal structure of the human ubiquitin-activating enzyme 5 (UBA5) bound to ATP: mechanistic insights into a minimalistic E1 enzyme. Bacik, J.P., Walker, J.R., Ali, M. et al. J Biol Chem (2010) 285:20273-20280. DOI 10.1074/jbc.M110.102921 · PubMed

Other PDB entries of the same protein (UniProt Q9GZZ9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5IAA 1.85 Å, Crystal structure of human UBA5 in complex with UFM1
7NW1 1.95 Å, Crystal structure of UFC1 in complex with UBA5
5IA8 2.0 Å, Structure of a Ubiquitin like protein with an E1 fragment
5L95 2.1 Å, Crystal structure of human UBA5 in complex with UFM1 and AMP
6H77 2.1 Å, E1 enzyme for ubiquitin like protein activation in complex with UBL
3GUC 2.25 Å, Human Ubiquitin-activating Enzyme 5 in Complex with AMPPNP
5HKH 2.55 Å, Crystal structure of Ufm1 in complex with UBA5
7NVK 2.65 Å, Crystal structure of UBA5 fragment fused to the N-terminus of UFC1
6H78 2.7 Å, E1 enzyme for ubiquitin like protein activation.
6H8C Structure of the human GABARAPL2 protein in complex with the UBA5 LIR motif
7OVC Structure of the human UFC1 protein in complex with the UBA5 C-terminal UFC1-binding…

Browse structure collections

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