6SYF: Human Ubc9 with covalent isopeptide ligand

Human Ubc9 with covalent isopeptide ligand. Determined by X-ray diffraction at 1.9 Å resolution. Released 12 Aug 2020.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 12
Atoms: 5,858
Mol. weight: 76.16 kDa
Released: 12 Aug 2020

Explore 6SYF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6SYF contains 33 α-helices and 36 β-strands across 8 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.

Chains A and D: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-18	13
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
α-helix	80-81	2
β-strand	86	1	2
β-strand	91	1	1
β-strand	92	1	2
β-strand	94	1	3
α-helix	95-97	3
α-helix	109-121	13
α-helix	131-139	9
α-helix	141-154	14

Chain B: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-18	16
β-strand	25-30	6	4
α-helix	31	1
β-strand	36-46	11	4
α-helix	47-48	2
β-strand	57-63	7	4
α-helix	72-73	2
β-strand	74-77	4	4
α-helix	80-81	2
β-strand	86	1	5
β-strand	91	1	4
β-strand	92	1	5
β-strand	94	1	6
α-helix	95-97	3
α-helix	109-121	13
α-helix	131-139	9
α-helix	141-154	14

Chain C: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-18	16
β-strand	25-30	6	7
β-strand	36-46	11	7
α-helix	47-48	2
β-strand	57-63	7	7
α-helix	72-73	2
β-strand	74-77	4	7
α-helix	80-81	2
β-strand	86	1	8
β-strand	91	1	7
β-strand	92	1	8
β-strand	94	1	9
α-helix	95-97	3
α-helix	109-121	13
α-helix	131-139	9
α-helix	141-154	14

Chains E, G, I and K: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	6	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SUMO-conjugating enzyme UBC9	A, B, C, D	protein	158	Homo sapiens	P63279 (AlphaFold model)
Ace-leu-arg-leu-arg-gly-cys	E, G, I, K	protein	7	Homo sapiens
Ace-ile-lys-gln-glu	F, H, J, L	protein	5	Homo sapiens

Sequence of entity 1 (A, B, C, D), FASTA

>6SYF_1 SUMO-conjugating enzyme UBC9 (chains A, B, C, D)
GSGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGAAGTPWAGGLFKL
RMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELL
NEPNIQDPAQAEAYTIYAQNRVEYEKRVRAQAKKFAPS

Sequence of entity 2 (E, G, I, K), FASTA

>6SYF_2 ACE-LEU-ARG-LEU-ARG-GLY-CYS (chains E, G, I, K)
XLRLRGC

Sequence of entity 3 (F, H, J, L), FASTA

>6SYF_3 ACE-ILE-LYS-GLN-GLU (chains F, H, J, L)
XIKQE

Primary citation

Lysine acylation using conjugating enzymes for site-specific modification and ubiquitination of recombinant proteins. Hofmann, R., Akimoto, G., Wucherpfennig, T.G. et al. Nat Chem (2020) 12:1008-1015. DOI 10.1038/s41557-020-0528-y · 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
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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