9E83: Transmembrane protease serine 2

TMPRSS2 crystal structure following acylation by UCSF_157. Determined by X-ray diffraction at 2.07 Å resolution. Released 25 Dec 2024.

Method: X-ray diffraction
Resolution: 2.07 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,708
Mol. weight: 40.69 kDa
Ligands: VU4, CIT
Released: 25 Dec 2024

Explore 9E83 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E83 contains 11 α-helices and 31 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: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	150-152	3	6
α-helix	153-155	3
β-strand	157-161	5	6
β-strand	168-170	3	6
β-strand	171	1	7
β-strand	172	1	8
α-helix	178-188	11
β-strand	196	1	9
β-strand	199-200	2	8
β-strand	210	1	7
β-strand	236-237	2	8
β-strand	238	1	6
β-strand	240	1	9

Chain B: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	257	1	1
β-strand	260-261	2	2
α-helix	262-263	2
β-strand	270-275	6	3
β-strand	278-285	8	3
β-strand	290-293	4	3
α-helix	295-298	4
α-helix	305-307	3
β-strand	309-312	4	3
β-strand	316	1	4
α-helix	317-319	3
β-strand	326-333	8	3
β-strand	338	1	5
β-strand	343	1	5
β-strand	347-351	5	3
α-helix	363-364	2
β-strand	365	1	2
α-helix	366-368	3
β-strand	378-383	6	2
α-helix	392-394	3
β-strand	396	1	4
β-strand	398-405	8	2
α-helix	407-410	4
β-strand	424-428	5	2
β-strand	435	1	1
β-strand	444-449	6	2
β-strand	452-461	10	2
β-strand	472-476	5	2
α-helix	477-490	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transmembrane protease serine 2	B	protein	249	Homo sapiens	O15393 (AlphaFold model)
Transmembrane protease serine 2 non-catalytic chain	A	protein	110	Homo sapiens	O15393 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9E83_1 Transmembrane protease serine 2 (chains B)
IVGGESALPGAWPWQVSLHVQNVHVCGGSIITPEWIVTAAHCVEKPLNNPWHWTAFAGIL
RQSFMFYGAGYQVEKVISHPNYDSKTKNNDIALMKLQKPLTFNDLVKPVCLPNPGMMLQP
EQLCWISGWGATEEKGKTSEVLNAAKVLLIETQRCNSRYVYDNLITPAMICAGFLQGNVD
SCQGDSGGPLVTSKNNIWWLIGDTSWGSGCAKAYRPGVYGNVMVFTDWIYRQMRADGEFV
EHHHHHHHH

Sequence of entity 2 (A), FASTA

>9E83_2 Transmembrane protease serine 2 non-catalytic chain (chains A)
AACVRLYGPNFILQVYSSQRKSWHPVCQDDWNENYGRAACRDMGYKNNFYSSQGIVDDSG
STSFMKLNTSAGNVDIYKKLYHSDACSSKAVVSLRCIACGVNLNDDDDDK

Ligands and cofactors

ID	Name	Formula	Copies
VU4	4-(2-aminoethyl)benzoic acid	C9 H11 N O2	1
CIT	Citric acid	C6 H8 O7	1

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

Primary citation

Large Library Docking and Biophysical Analysis of Small-Molecule TMPRSS2 Inhibitors. Fraser, B.J., Young, N.J., Bender, B.J. et al. J Med Chem (2025) 68:19893-19907. DOI 10.1021/acs.jmedchem.4c03089 · PubMed

Other PDB entries of the same protein (UniProt O15393 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8V04 1.58 Å, High resolution TMPRSS2 structure following acylation by nafamostat
8S0L 1.8 Å, Crystal structure of the TMPRSS2 zymogen in complex with the nanobody A07
9JD1 1.9 Å, Crystal structure of TMPRSS2 in complex with Fab
7MEQ 1.95 Å, Crystal structure of human TMPRSS2 in complex with Nafamostat
9JD0 2.0 Å, Crystal structure of TMPRSS2 in complex with nanobody
9U8G 2.0 Å, Crystal structure of TMPRSS2 in complex with nanobody77_10
8V1F 2.19 Å, TMPRSS2 complexed with the noncovalent inhibitor 6-amidino-2-napthol
8S0N 2.3 Å, Crystal structure of the TMPRSS2 zymogen in complex with the nanobody A07
7Y0E 2.39 Å, Crystal structure of TMPRSS2 in complex with Camostat
8HD8 2.4 Å, Crystal structure of TMPRSS2 in complex with 212-148
9IZN 2.4 Å, Crystal structure of HKU1A RBD bound to TMPRSS2
7XYD 2.58 Å, Crystal structure of TMPRSS2 in complex with Nafamostat

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