13SK: E3 ubiquitin-protein ligase MYLIP

Name: PDB 13SK: PanDDA analysis group deposition -- IDOL RING domain in complex with Z2692078340
Published: 2025-12-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

PanDDA analysis group deposition -- IDOL RING domain in complex with Z2692078340. Determined by X-ray diffraction at 1.54 Å resolution. Released 10 Dec 2025.

Method: X-ray diffraction
Resolution: 1.54 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,685
Mol. weight: 36.63 kDa
Ligands: ZN, W1Y
Released: 10 Dec 2025

Explore 13SK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

13SK contains 8 α-helices and 36 β-strands across 4 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 B: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	369-383	15
β-strand	386	1	1
β-strand	394	1	1
β-strand	397-400	4	2
β-strand	404	1	3
β-strand	407	1	2
α-helix	409-413	5
β-strand	417	1	4
β-strand	424	1	4
β-strand	427-430	4	2
β-strand	432	1	5

Chain C: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	369-383	15
β-strand	386	1	9
β-strand	394	1	9
β-strand	397-400	4	10
β-strand	404	1	11
β-strand	407	1	10
α-helix	409-412	4
β-strand	417	1	12
β-strand	424	1	12
β-strand	427-430	4	10
β-strand	432	1	13

Chain D: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	369-384	16
β-strand	386	1	14
β-strand	394	1	14
β-strand	397-400	4	15
β-strand	404	1	13
β-strand	407	1	15
α-helix	409-413	5
β-strand	417	1	16
β-strand	424	1	16
β-strand	427-430	4	15
β-strand	432	1	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase MYLIP	A, B, C, D	protein	78	Homo sapiens	Q8WY64 (AlphaFold model)

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

>13SK_1 E3 ubiquitin-protein ligase MYLIP (chains A, B, C, D)
SQQTRVLQEKLRKLKEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQSCPVCRSRVEH
VQHVYLPTHTSLLNLTVI

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8
W1Y	N-methyl-1-(1-phenyl-1H-pyrazol-4-yl)methanamine	C11 H13 N3	4

Water and common crystallization additives (DMS) are not listed.

Primary citation

PanDDA analysis group deposition. Bradshaw, W.J., Guenther, F., Murphy, E.J. To be published.

Other PDB entries of the same protein (UniProt Q8WY64 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9SA1 1.06 Å, The RING domain of IDOL
9SA2 1.1 Å, The RING domain of IDOL
13SY 1.29 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with POB0041
13SQ 1.3 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with Z369936976
13SL 1.34 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with Z275151340
13SX 1.36 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with POB0134
13ST 1.37 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with Z608065044
13SW 1.37 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with POB0087
13SM 1.4 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with Z275179946
13SE 1.44 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with Z1587220559
13SN 1.44 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with Z2757439080
13SJ 1.47 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with Z2643472210

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