4W5V: Human SUMO E2-conjugating enzyme

Crystal structure of Human SUMO E2-conjugating enzyme (Ubc9) in complex with E1-activating enzyme (Uba2) ubiquitin fold domain (Ufd). Determined by X-ray diffraction at 2.5 Å resolution. Released 9 Sept 2015.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,179
Mol. weight: 31.98 kDa
Released: 9 Sept 2015

Explore 4W5V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4W5V contains 10 α-helices and 17 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: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	2-18	17
β-strand	25-30	6	1
α-helix	31	1
β-strand	36-46	11	1
α-helix	47-48	2
β-strand	57-63	7	1
β-strand	74-77	4	1
β-strand	86	1	2
β-strand	91	1	1
β-strand	92	1	2
α-helix	95-97	3
β-strand	98	1	3
β-strand	101	1	3
α-helix	109-121	13
α-helix	131-138	8
α-helix	141-154	14

Chain B: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	449-454	6	1
β-strand	460	1	4
α-helix	461-463	3
α-helix	464-472	9
β-strand	478-482	5	1
β-strand	488-491	4	1
β-strand	505	1	4
α-helix	506-509	4
β-strand	516-521	6	1
β-strand	527-534	8	1
β-strand	544-547	4	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SUMO-conjugating enzyme UBC9	A	protein	163	Homo sapiens	P63279 (AlphaFold model)
SUMO-activating enzyme subunit 2	B	protein	122	Homo sapiens	Q9UBT2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4W5V_1 SUMO-conjugating enzyme UBC9 (chains A)
GPLGSMSGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGKKGTPWEG
GLFKLRMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLG
IQELLNEPNIQDPAQAEAYTIYCQNRVEYEKRVRAQAKKFAPS

Sequence of entity 2 (B), FASTA

>4W5V_2 SUMO-activating enzyme subunit 2 (chains B)
GPLGSASKPEVTVRLNVHKVTVLTLQDKIVKEKFAMVAPDVQIEDGKGTILISSEEGETE
ANNHKKLSEFGIRNGSRLQADDFLQDYTLLINILHSEDLGKDVEFEVVGDAPEKVGPKQA
ED

Primary citation

Crystal structure of human SUMO complex. Reiter, K.H., Boucher, L.E., Bosch, J. et al. To be published.

Other PDB entries of the same protein (UniProt P63279 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5F6E 1.12 Å, Crystal Structure of human Ubc9 (K48A/K49A/E54A)
5F6Y 1.14 Å, Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole)
2GRR 1.3 Å, Crystal Structure of human RanGAP1-Ubc9-D127S
5F6V 1.49 Å, Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 1 (biphenol from…
5F6U 1.55 Å, Crystal Structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 8 (JSS190B146)
5F6D 1.55 Å, Crystal structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 6
5F6X 1.56 Å, Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole…
5F6W 1.7 Å, Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 1 (biphenol)
2GRO 1.7 Å, Crystal Structure of human RanGAP1-Ubc9-N85Q
2GRQ 1.7 Å, Crystal Structure of human RanGAP1-Ubc9-D127A
9GLR 1.72 Å, Crystal Structure of Human UBC9 C93E
2GRN 1.8 Å, Crystal Structure of human RanGAP1-Ubc9

Browse structure collections

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