9FPA: Ubiquitin

DUBS Parachlamydia sp. PcJOS orthorhombic crystal form. Determined by X-ray diffraction at 2.18 Å resolution. Released 23 Apr 2025.

Method: X-ray diffraction
Resolution: 2.18 Å
Organisms: Homo sapiens, Parachlamydia sp.
Chains: 3
Atoms: 4,940
Mol. weight: 73.86 kDa
Ligands: CIT
Released: 23 Apr 2025

Explore 9FPA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9FPA contains 32 α-helices and 40 β-strands across 3 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: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	98-100	3
α-helix	103-107	5
α-helix	111-121	11
β-strand	123	1	10
β-strand	125	1	11
β-strand	128	1	11
α-helix	134-138	5
α-helix	154-156	3
α-helix	162-171	10
α-helix	178-193	16
α-helix	197-205	9
β-strand	212	1	3
α-helix	214-225	12
β-strand	229-233	5	12
α-helix	234-236	3
α-helix	244-252	9
β-strand	257-262	6	12
β-strand	268	1	10
β-strand	280	1	10
β-strand	284-290	7	12
β-strand	296-299	4	12
β-strand	307-308	2	12
α-helix	311-313	3
β-strand	319-323	5	12

Chain B: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
β-strand	55	1	2
α-helix	57-59	3
β-strand	66-71	6	1
β-strand	73	1	3
β-strand	77-82	6	4
β-strand	88-93	6	4
β-strand	98	1	5
α-helix	99-110	12
α-helix	114-116	3
β-strand	117-121	5	4
β-strand	124-125	2	4
α-helix	126-127	2
β-strand	131	1	5
α-helix	133-135	3
β-strand	142-147	6	4
β-strand	148	1	6

Chain C: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	98-100	3
α-helix	103-107	5
α-helix	111-121	11
β-strand	123	1	7
α-helix	134-138	5
β-strand	141	1	8
α-helix	146-147	2
α-helix	162-171	10
α-helix	178-192	15
α-helix	198-205	8
α-helix	207-209	3
β-strand	211	1	6
α-helix	214-225	12
β-strand	229-233	5	9
α-helix	234-236	3
α-helix	244-252	9
β-strand	257-261	5	9
β-strand	268	1	7
β-strand	280	1	7
β-strand	285-290	6	9
β-strand	296-299	4	9
β-strand	307-308	2	9
β-strand	309	1	8
α-helix	311-313	3
β-strand	319-323	5	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin	B	protein	152	Homo sapiens	F5H388 (AlphaFold model)
Peptidase C39-like domain-containing protein	A, C	protein	255	Parachlamydia sp.	A0A2H9SU66 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9FPA_1 Ubiquitin (chains B)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLI
FAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Sequence of entity 2 (A, C), FASTA

>9FPA_2 Peptidase C39-like domain-containing protein (chains A, C)
KTQPSTTQKVENTAKTLFKPDLKSPPMNPQWLTEEQIKKMSPDEQGNLIDTYAARKINAA
SDLTHAQLRGMIGSTAASHIAIVNAQETGLGHAGRYAINNALQQEALSQNEFLSLTGQIF
SNQLGMSLADVKNLIQNQDDFGIDTGVLAQILKQKFNQPVKESKICDLPDCALSKQQAVE
NYIGKAKWVIVANIGTEVFDMPSSTHAVYPLTRGHFVALRRDADNRWWYLDSRGKNPVNI
ALAIIPRTCTLIVPL

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	2

Primary citation

A family of bacterial Josephin-like deubiquitinases with an irreversible cleavage mode. Hermanns, T., Kolek, S., Uthoff, M. et al. Mol Cell (2025) 85:1202-1215.e5. DOI 10.1016/j.molcel.2025.02.002 · PubMed

Other PDB entries of the same protein (UniProt F5H388 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8ST7 1.44 Å, Structure of E3 ligase VsHECT bound to ubiquitin
4I6N 1.7 Å, Crystal structure of Trichinella spiralis UCH37 catalytic domain bound to Ubiquitin…
6W9R 1.82 Å, Crystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to…
8RQI 1.94 Å, Structure of Rhizobium NopD with ubiquitin
4IG7 2.0 Å, Crystal structure of Trichinella spiralis UCH37 bound to Ubiquitin vinyl methyl ester
4PQT 2.05 Å, Insights into the mechanism of deubiquitination by JAMM deubiquitinases from co-crystal…
6W9S 2.1 Å, Crystal structure of an OTU deubiquitinase from Escherichia albertii bound to ubiquitin
9FN4 2.15 Å, DUBS Parachlamydia sp. PcJOS
6NN6 3.9 Å, Structure of Dot1L-H2BK120ub nucleosome complex

Browse structure collections

About this viewer

MolViewer shows 9FPA directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.