9S3J: PDB entry 9S3J

Crystal structure of the human tumor necrosis factor receptor 1 extracellular domain in complex with a picolinic acid based ligand at 1.77A resolution. Determined by X-ray diffraction at 1.77 Å resolution. Released 1 Jul 2026.

Method: X-ray diffraction
Resolution: 1.77 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,277
Mol. weight: 38.2 kDa
Ligands: A1JLJ, PO4
Released: 1 Jul 2026

Explore 9S3J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9S3J contains 18 α-helices and 40 β-strands across 2 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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	16	1
β-strand	19-21	3	1
β-strand	29-31	3	1
α-helix	32	1
β-strand	33	1	2
α-helix	34	1
β-strand	37-41	5	3
β-strand	48	1	4
α-helix	49-50	2
β-strand	51-54	4	3
α-helix	55-56	2
β-strand	59-60	2	5
β-strand	65	1	2
α-helix	70	1
β-strand	71-72	2	5
α-helix	73-76	4
α-helix	78-80	3
β-strand	83-86	4	6
β-strand	89	1	7
β-strand	92	1	7
β-strand	95-97	3	6
β-strand	102-106	5	8
β-strand	112-116	5	8
α-helix	117-118	2
β-strand	124-127	4	9
β-strand	130	1	10
β-strand	133	1	10
β-strand	136-138	3	9

Chain B: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	15-16	2
β-strand	19-21	3	11
β-strand	29-31	3	11
α-helix	32	1
β-strand	33	1	12
α-helix	34	1
β-strand	37-41	5	13
β-strand	48	1	4
α-helix	49-50	2
β-strand	51-54	4	13
α-helix	55-56	2
β-strand	59-60	2	14
β-strand	65	1	12
α-helix	70	1
β-strand	71-72	2	14
α-helix	73-76	4
α-helix	78-80	3
β-strand	83-86	4	15
β-strand	89	1	16
β-strand	92	1	16
β-strand	95-97	3	15
β-strand	102-108	7	17
β-strand	111-116	6	17
α-helix	117-119	3
β-strand	123-127	5	18
β-strand	130	1	19
β-strand	133	1	19
β-strand	136-139	4	18
β-strand	144-145	2	20
β-strand	150-151	2	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor receptor superfamily member 1A, membrane form	A, B	protein	164	Homo sapiens	P19438 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9S3J_1 Tumor necrosis factor receptor superfamily member 1A, membrane form (chains A, B)
GPRDSVCPQGKYIHPQNNSICCTKCHKGTYLYNDCPGPGQDTDCRECESGSFTASENHLR
HCLSCSKCRKEMGQVEISSCTVDRDTVCGCRKNQYRHYWSENLFQCFNCSLCLNGTVHLS
CQEKQNTVCTCHAGFFLRENECVSCSNCKKSLECTKLCLPQIEN

Ligands and cofactors

ID	Name	Formula	Copies
A1JLJ	4-(4-fluorophenyl)pyridine-2-carboxylic acid	C12 H8 F N O2	1
PO4	Phosphate ion	O4 P	10

Primary citation

Discovery of Ligands for the TNFR1 Extracellular Domain Using Fragment-Based Drug Discovery. Chedotal, H., Povlsen, K., Narayanan, D. et al. ChemMedChem (2026) 21:e70365-e70365. DOI 10.1002/cmdc.70365 · PubMed

Other PDB entries of the same protein (UniProt P19438 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8P6Q 1.4 Å, Racemic structure of TNFR1 cysteine-rich domain
9S3I 1.64 Å, Crystal structure of the human tumor necrosis factor receptor 1 extracellular domain at…
1EXT 1.85 Å, Extracellular domain of the 55KDA tumor necrosis factor receptor. Crystallized at PH3.7…
1NCF 2.25 Å, A new paradigm for tumor necrosis factor signalling
8ZUI 2.56 Å, Binary cluster of TNF-TNFR1 ectodomain complex
9V9C 2.62 Å, Cryo-EM structure of human TNFR1 DD filament
7KP7 2.65 Å, asymmetric mTNF-alpha hTNFR1 complex
1TNR 2.85 Å, Crystal structure of the soluble human 55 kd tnf receptor-human tnf-beta complex:…
1FT4 2.9 Å, Photochemically-enhanced binding of small molecules to the tumor necrosis factor…
7KPB 3.0 Å, Human TNF-alpha TNFR1 complex bound to conformationally selective antibody
7KP8 3.15 Å, asymmetric mTNF-alpha hTNFR1 complex
9VIN 3.41 Å, Ternary complex of TNFR1-DD, TRADD-DD and RIPK1-DD

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