5F6X: Ubc9

Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole from cocktail screen). Determined by X-ray diffraction at 1.56 Å resolution. Released 27 Apr 2016.

Method: X-ray diffraction
Resolution: 1.56 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,594
Mol. weight: 17.91 kDa
Ligands: 5VM
Released: 27 Apr 2016

Explore 5F6X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5F6X contains 7 α-helices and 7 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: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-18	16
β-strand	25-30	6	1
β-strand	36-46	11	1
α-helix	47-48	2
β-strand	57-63	7	1
α-helix	72-73	2
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
α-helix	109-121	13
α-helix	131-139	9
α-helix	141-154	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SUMO-conjugating enzyme UBC9	A	protein	157	Homo sapiens	P63279 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5F6X_1 SUMO-conjugating enzyme UBC9 (chains A)
SGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGAAGTPWAGGLFKLR
MLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELLN
EPNIQDPAQAEAYTIYCQNRVEYEKRVRAQAKKFAPS

Ligands and cofactors

ID	Name	Formula	Copies
5VM	5-chloranyl-3~{H}-1,3-benzoxazole-2-thione	C7 H4 Cl N O S	1

Primary citation

Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9. Hewitt, W.M., Lountos, G.T., Zlotkowski, K. et al. Angew Chem Int Ed Engl (2016) 55:5703-5707. DOI 10.1002/anie.201511351 · PubMed

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
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
6SYF 1.9 Å, Human Ubc9 with covalent isopeptide ligand

Browse structure collections

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