7XYD: TMPRSS2

Crystal structure of TMPRSS2 in complex with Nafamostat. Determined by X-ray diffraction at 2.58 Å resolution. Released 6 Dec 2023.

Method: X-ray diffraction
Resolution: 2.58 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,833
Mol. weight: 88.7 kDa
Ligands: GBS, CA, NAG
Released: 6 Dec 2023

Explore 7XYD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7XYD contains 25 α-helices and 65 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: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	118	1	1
β-strand	127	1	1
α-helix	129-131	3
β-strand	149-152	4	2
β-strand	157-162	6	2
β-strand	167-170	4	2
β-strand	171	1	3
β-strand	172	1	2
α-helix	178-187	10
β-strand	196-200	5	2
β-strand	209-212	4	3
β-strand	225-228	4	3
β-strand	236-240	5	2

Chain B: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	117	1
β-strand	118-119	2	9
β-strand	126-127	2	9
α-helix	129-131	3
β-strand	149-152	4	10
β-strand	157-162	6	10
α-helix	164-166	3
β-strand	167-170	4	10
β-strand	171	1	11
β-strand	172	1	12
α-helix	178-187	10
β-strand	196-197	2	13
β-strand	200	1	12
β-strand	209-212	4	11
α-helix	221-223	3
β-strand	225-228	4	11
β-strand	236	1	12
β-strand	238	1	10
β-strand	239-240	2	13

Chain C: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	257	1	4
β-strand	260-261	2	5
α-helix	262-263	2
β-strand	270-275	6	6
β-strand	278-287	10	6
β-strand	290-293	4	6
α-helix	295-298	4
α-helix	305-307	3
β-strand	309-312	4	6
β-strand	316	1	7
α-helix	317-319	3
β-strand	326-333	8	6
β-strand	338	1	8
β-strand	343	1	8
β-strand	347-351	5	6
α-helix	363-364	2
β-strand	365	1	5
α-helix	366-368	3
β-strand	378-383	6	5
α-helix	392-394	3
β-strand	396	1	7
β-strand	398-405	8	5
α-helix	407-410	4
β-strand	424-428	5	5
β-strand	435	1	4
β-strand	444-449	6	5
β-strand	452-461	10	5
β-strand	472-476	5	5
α-helix	477-494	18

Chain D: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	257	1	14
β-strand	260-261	2	15
α-helix	262-263	2
β-strand	270-275	6	16
β-strand	278-285	8	16
β-strand	290-293	4	16
α-helix	295-298	4
α-helix	305-307	3
β-strand	309-312	4	16
β-strand	316	1	17
α-helix	317-319	3
β-strand	326-333	8	16
β-strand	338	1	18
β-strand	343	1	18
β-strand	347-351	5	16
α-helix	363-364	2
β-strand	365	1	15
α-helix	366-368	3
β-strand	378-383	6	15
α-helix	392-394	3
β-strand	396	1	17
β-strand	398-405	8	15
α-helix	407-410	4
β-strand	424-428	5	15
β-strand	435	1	14
β-strand	444-449	6	15
β-strand	452-461	10	15
β-strand	472-476	5	15
α-helix	477-492	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transmembrane protease serine 2 catalytic chain	A, B	protein	146	Homo sapiens	O15393 (AlphaFold model)
Transmembrane protease serine 2 catalytic chain	C, D	protein	249	Homo sapiens	O15393 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7XYD_1 Transmembrane protease serine 2 catalytic chain (chains A, B)
MGSKCSNSGIECDSSGTCINPSNWCDGVSHCPGGEDENRCVRLYGPNFILQVYSSQRKSW
HPVCQDDWNENYGRAACRDMGYKNNFYSSQGIVDDSGSTSFMKLNTSAGNVDIYKKLYHS
DACSSKAVVSLRCIACGVNLNDDDDK

Sequence of entity 2 (C, D), FASTA

>7XYD_2 Transmembrane protease serine 2 catalytic chain (chains C, D)
IVGGESALPGAWPWQVSLHVQNVHVCGGSIITPEWIVTAAHCVEKPLNNPWHWTAFAGIL
RQSFMFYGAGYQVEKVISHPNYDSKTKNNDIALMKLQKPLTFNDLVKPVCLPNPGMMLQP
EQLCWISGWGATEEKGKTSEVLNAAKVLLIETQRCNSRYVYDNLITPAMICAGFLQGNVD
SCQGDSGGPLVTSKNNIWWLIGDTSWGSGCAKAYRPGVYGNVMVFTDWIYRQMRADGEFV
EHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
GBS	4-carbamimidamidobenzoic acid	C8 H9 N3 O2	2
CA	Calcium ion	Ca	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Structure-based discovery of dual pathway inhibitors for SARS-CoV-2 entry. Wang, H., Yang, Q., Liu, X. et al. Nat Commun (2023) 14:7574-7574. DOI 10.1038/s41467-023-42527-5 · 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
9E83 2.07 Å, TMPRSS2 crystal structure following acylation by UCSF_157
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

Browse structure collections

About this viewer

MolViewer shows 7XYD 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.