9NN9: ISG15

ISG15 complexed with nanobody. Determined by X-ray diffraction at 2.59 Å resolution. Released 1 Oct 2025.

Method: X-ray diffraction
Resolution: 2.59 Å
Organisms: Homo sapiens, Vicugna pacos
Chains: 6
Atoms: 6,505
Mol. weight: 103.69 kDa
Released: 1 Oct 2025

Explore 9NN9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9NN9 contains 36 α-helices and 70 β-strands across 6 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: 8 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
β-strand	14-18	5	1
α-helix	25-36	12
α-helix	40-42	3
β-strand	43-47	5	1
α-helix	52	1
β-strand	53	1	1
α-helix	54-55	2
β-strand	70-75	6	1
β-strand	82-87	6	2
β-strand	93-98	6	2
β-strand	103	1	3
α-helix	104-115	12
α-helix	119-121	3
β-strand	122-126	5	2
β-strand	129-130	2	2
α-helix	131-132	2
β-strand	136	1	3
α-helix	137-140	4
β-strand	147-152	6	2

Chain B: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	4
β-strand	10-13	4	5
β-strand	18-24	7	4
β-strand	33-39	7	5
β-strand	46-51	6	5
β-strand	58-60	3	5
α-helix	62-64	3
β-strand	68-73	6	4
α-helix	74-76	3
β-strand	78-83	6	4
α-helix	88-90	3
β-strand	92-99	8	5
α-helix	105-106	2
β-strand	108-110	3	5
β-strand	114-119	6	5

Chain C: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	6
α-helix	10-12	3
β-strand	14-18	5	6
α-helix	25-36	12
α-helix	40-42	3
β-strand	43-47	5	6
α-helix	52	1
β-strand	53	1	6
α-helix	54	1
α-helix	60-62	3
β-strand	70-75	6	6
β-strand	82-87	6	7
β-strand	93-98	6	7
β-strand	103	1	8
α-helix	104-115	12
α-helix	119-121	3
β-strand	122-126	5	7
β-strand	129-130	2	7
α-helix	131-132	2
β-strand	136	1	8
α-helix	137-140	4
β-strand	147-152	6	7

Chain D: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	12-13	2	10
β-strand	18-25	8	9
β-strand	33-39	7	11
β-strand	46-51	6	11
β-strand	58-60	3	11
β-strand	68-73	6	9
β-strand	78-83	6	9
α-helix	88-90	3
β-strand	92-99	8	11
β-strand	108-110	3	11
β-strand	114-116	3	11
β-strand	118-119	2	10

Chain E: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	12
β-strand	14-18	5	12
α-helix	25-36	12
α-helix	40-42	3
β-strand	43-47	5	12
α-helix	52	1
β-strand	53	1	12
α-helix	54-55	2
α-helix	60-63	4
β-strand	69-75	7	12
β-strand	82-87	6	13
β-strand	93-98	6	13
β-strand	103	1	14
α-helix	104-115	12
α-helix	119-121	3
β-strand	122-126	5	13
β-strand	129-130	2	13
α-helix	131-132	2
β-strand	136	1	14
α-helix	137-140	4
β-strand	147-152	6	13

Chain F: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	15
β-strand	10-13	4	16
β-strand	18-25	8	15
β-strand	33-39	7	16
α-helix	44-45	2
β-strand	46-51	6	16
β-strand	58-60	3	16
β-strand	68-73	6	15
α-helix	74-76	3
β-strand	78-83	6	15
α-helix	88-90	3
β-strand	92-99	8	16
α-helix	105-106	2
β-strand	108-110	3	16
β-strand	114-119	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-like protein ISG15	A, C, E	protein	165	Homo sapiens	P05161 (AlphaFold model)
Nanobody	B, D, F	protein	149	Vicugna pacos

Sequence of entity 1 (A, C, E), FASTA

>9NN9_1 Ubiquitin-like protein ISG15 (chains A, C, E)
MGWDLTVKMLAGNEFQVSLSSSMSVSELKAQITQKIGVHAFQQRLAVHPSGVALQDRVPL
ASQGLGPGSTVLLVVDKSDEPLSILVRNNKGRSSTYEVRLTQTVAHLKQQVSGLEGVQDD
LFWLTFEGKPLEDQLPLGEYGLKPLSTVFMNLRLRGGSSHHHHHH

Sequence of entity 2 (B, D, F), FASTA

>9NN9_2 Nanobody (chains B, D, F)
QLQLVETGGGLVQAGGSLRLSCAASGRTFAGLSVKWFRQPPGAEREWVAHITSTGSSTHY
ADSVKGRFTISRDYDRNMVYLQMSSLKPEDTAVYYCHASTLWPEKHQDYWGQGIQVTVSS
GGLPETGGSSYPYDVPDYAGGSSHHHHHH

Primary citation

Identification and characterization of nanobodies specific for the human ubiquitin-like ISG15 protein. Gan, J., Dabhade, P., Wijne, C. et al. J Biol Chem (2025) 301:110564-110564. DOI 10.1016/j.jbc.2025.110564 · PubMed

Other PDB entries of the same protein (UniProt P05161 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6FFA 1.5 Å, FMDV Leader protease bound to substrate ISG15
3PHX 1.6 Å, OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with ISG15
3RT3 2.01 Å, Complex of influenza virus protein with host anti-viral factor
7S6P 2.15 Å, The crystal structure of human ISG15
3SDL 2.29 Å, Crystal structure of human ISG15 in complex with NS1 N-terminal region from influenza B…
6BI8 2.29 Å, X-ray structure of MERS coronavirus papain-like protease in complex with human ISG15
3PSE 2.3 Å, Structure of a viral OTU domain protease bound to interferon-stimulated gene 15 (ISG15)
3R66 2.3 Å, Crystal structure of human ISG15 in complex with NS1 N-terminal region from influenza…
5W8U 2.41 Å, Crystal structure of MERS-CoV papain-like protease in complex with the C-terminal domain…
1Z2M 2.5 Å, Crystal Structure of ISG15, the Interferon-Induced Ubiquitin Cross Reactive Protein
5TL6 2.62 Å, Crystal structure of SARS-CoV papain-like protease in complex with the C-terminal domain…
9LW4 2.7 Å, UbCh8-ISG15 complex

Browse structure collections

About this viewer

MolViewer shows 9NN9 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.