4LDT: H/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub

The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub. Determined by X-ray diffraction at 1.9 Å resolution. Released 14 Aug 2013.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Homo sapiens, Caenorhabditis elegans
Chains: 4
Atoms: 4,832
Mol. weight: 67 kDa
Ligands: MG
Released: 14 Aug 2013

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

Secondary structure: helices and β-sheets

4LDT contains 33 α-helices and 32 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: 16 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	20-40	21
β-strand	44	1	1
α-helix	45-47	3
β-strand	48-49	2	2
α-helix	51-55	5
α-helix	63-72	10
β-strand	76-80	5	2
β-strand	82	1	1
α-helix	88-103	16
α-helix	105-124	20
α-helix	129-147	19
α-helix	153-161	9
α-helix	163-183	21
α-helix	185-188	4
α-helix	189-191	3
α-helix	198-201	4
α-helix	202-206	5
α-helix	211-212	2
β-strand	213	1	3
α-helix	215-224	10
β-strand	229-233	5	2
β-strand	244-248	5	2
α-helix	255-257	3
β-strand	259-264	6	2
β-strand	266	1	3
β-strand	267-273	7	2

Chain B: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	4
β-strand	12-16	5	4
β-strand	22	1	5
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	4
β-strand	48-49	2	4
α-helix	50-51	2
β-strand	55	1	5
β-strand	66-71	6	4
β-strand	75	1	3

Chain C: 8 helices, 7 β-strands

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

Chain D: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	8
α-helix	11	1
β-strand	12-16	5	8
β-strand	22	1	9
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	8
β-strand	48-49	2	8
α-helix	50-51	2
β-strand	55	1	9
α-helix	57-59	3
β-strand	66-71	6	8
α-helix	72-73	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin thioesterase otubain-like	A	protein	288	Homo sapiens, Caenorhabditis elegans	Q96FW1 (AlphaFold model), Q9XVR6 (AlphaFold model)
Ubiquitin aldehyde	B	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 D2	C	protein	148	Homo sapiens	P62837 (AlphaFold model)
Ubiquitin	D	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4LDT_1 Ubiquitin thioesterase otubain-like (chains A)
MAAEEPQQQKQEPLGSDSEGVNCLAYDEAIMAQQDRIQQEIAVQNPLVATLAPFSILCAE
YDNETSAAFLSKATELSEVYGEIRYIRGDGNCFYRAILVGLIEIMLKDRARLEKFIASSR
DWTRTLVELGFPDWTCTDFCDFFIEFLEKIHSGVHTEEAVYTILNDDGSANYILMFFRLI
TSAFLKQNSEEYAPFIDEGMTVAQYCEQEIEPMWKDADHLAINSLIKAAGTRVRIEYMDR
TAAPNGGWHYDIPSDDQQIAPEITLLYRPGHYDVIYKKDSTEASEIEN

Sequence of entity 2 (B), FASTA

>4LDT_2 Ubiquitin aldehyde (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (C), FASTA

>4LDT_3 Ubiquitin-conjugating enzyme E2 D2 (chains C)
GMALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTD
YPFKPPKVAFTTRIYHPNINSNGSISLDILRSQWSPALTISKVLLSICSLLCDPNPDDPL
VPEIARIYKTDREKYNRIAREWTQKYAM

Sequence of entity 4 (D), FASTA

>4LDT_4 Ubiquitin (chains D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

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

Primary citation

E2 ubiquitin-conjugating enzymes regulate the deubiquitinating activity of OTUB1. Wiener, R., Dibello, A.T., Lombardi, P.M. et al. Nat Struct Mol Biol (2013) 20:1033-1039. DOI 10.1038/nsmb.2655 · PubMed

Other PDB entries of the same protein (UniProt Q96FW1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2ZFY 1.69 Å, Crystal structure of human Otubain 1
4I6L 2.49 Å, Crystal structure of OTUB1 in complex with ubiquitin variant
4DHZ 3.11 Å, The structure of h/ceOTUB1-ubiquitin aldehyde-UBC13~Ub
3VON 3.15 Å, Crystalstructure of the ubiquitin protease
4DDG 3.3 Å, Crystal structure of human OTUB1/UbcH5b~Ub/Ub
4DDI 3.8 Å, Crystal structure of human OTUB1/UbcH5b~Ub/Ub

Browse structure collections

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