1X23: Ubch5c

Crystal structure of ubch5c. Determined by X-ray diffraction at 1.85 Å resolution. Released 3 May 2005.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,544
Mol. weight: 69.96 kDa
Released: 3 May 2005

Explore 1X23 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1X23 contains 30 α-helices and 29 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.

Chain A: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	-1-15	16
β-strand	21-25	5	1
β-strand	32-38	7	1
α-helix	39-40	2
β-strand	49-55	7	1
α-helix	64-65	2
β-strand	66-69	4	1
β-strand	75	1	2
β-strand	78	1	2
β-strand	83	1	1
β-strand	84	1	2
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Chain B: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	-1-15	16
α-helix	17-18	2
β-strand	21-26	6	3
β-strand	29-38	10	3
β-strand	49-55	7	3
α-helix	64-65	2
β-strand	66-69	4	3
β-strand	75	1	4
β-strand	78	1	4
β-strand	84	1	4
α-helix	87-89	3
α-helix	99-109	11
α-helix	121-129	9
α-helix	131-145	15

Chain C: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	-1-15	16
α-helix	17-18	2
β-strand	21-25	5	5
β-strand	32-38	7	5
α-helix	39-40	2
β-strand	49-55	7	5
α-helix	64-65	2
β-strand	66-69	4	5
β-strand	78	1	6
β-strand	83	1	5
β-strand	84	1	6
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Chain D: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	-6--4	3
α-helix	-1-15	16
β-strand	21-25	5	7
β-strand	32-38	7	7
α-helix	39-40	2
β-strand	49-55	7	7
α-helix	64-65	2
β-strand	66-69	4	7
β-strand	75	1	8
β-strand	78	1	8
β-strand	84	1	8
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D3	A, B, C, D	protein	155	Homo sapiens	P61077 (AlphaFold model)

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

>1X23_1 Ubiquitin-conjugating enzyme E2 D3 (chains A, B, C, D)
GPLGSPEFMALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFL
TIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCD
PNPDDPLVPEIARIYKTDRDKYNRISREWTQKYAM

Primary citation

Crystal structure of ubch5c. Nakanishi, M., Teshima, N., Mizushima, T. et al. To be published.

Other PDB entries of the same protein (UniProt P61077 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EGG 1.76 Å, Crystal structure of human ubiquitin-conjugating enzyme UBCH5C
4S3O 2.0 Å, PCGF5-RING1B-UbcH5c complex
8UQA 2.05 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker
5IFR 2.2 Å, Structure of the stable UBE2D3-UbDha conjugate
8UQ9 2.3 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker
8UQ8 2.34 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker
3UGB 2.35 Å, UbcH5c~Ubiquitin Conjugate
8AMS 2.4 Å, Complex of human TRIM2 RING domain, UBCH5C, and Ubiquitin
8UQB 2.48 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker…
6T7F 2.58 Å, RCR E3 ligase E2-Ubiquitin transthiolation intermediate
8UQC 2.61 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker…
3RPG 2.65 Å, Bmi1/Ring1b-UbcH5c complex structure

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