3NPS: Membrane-type serine protease 1

Crystal structure of membrane-type serine protease 1 (MT-SP1) in complex with the Fab Inhibitor S4. Determined by X-ray diffraction at 1.5 Å resolution. Released 6 Jul 2011.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,979
Mol. weight: 74.08 kDa
Released: 6 Jul 2011

Explore 3NPS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3NPS contains 29 α-helices and 64 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: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	2
β-strand	30-35	6	3
β-strand	39-46	8	3
β-strand	51-54	4	3
α-helix	56-59	4
β-strand	60B	1	4
β-strand	60E	1	4
α-helix	61-63	3
β-strand	64-68	5	3
β-strand	72	1	5
β-strand	81-90	10	3
β-strand	104-108	5	3
β-strand	122	1	2
α-helix	123-125	3
β-strand	135-140	6	2
β-strand	154	1	5
β-strand	156-162	7	2
α-helix	165-171	7
β-strand	180-184	5	2
β-strand	189	1	1
α-helix	197	1
β-strand	198-202	5	2
β-strand	207-215	9	2
β-strand	226-230	5	2
α-helix	232-234	3
α-helix	235-242	8

Chain B: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	6
α-helix	7-9	3
β-strand	10-12	3	7
β-strand	18-24	7	6
β-strand	32-39	8	7
β-strand	45-51	7	7
β-strand	58-59	2	7
α-helix	61-63	3
β-strand	67-72	6	6
α-helix	73-75	3
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-97	10	7
β-strand	100I-103	4	7
β-strand	107-111	5	7
α-helix	114-116	3
β-strand	117	1	8
α-helix	118-119	2
β-strand	120-124	5	9
α-helix	125-127	3
α-helix	130-131	2
β-strand	135-145	11	9
β-strand	146	1	8
β-strand	151-154	4	10
α-helix	155-157	3
β-strand	159	1	10
β-strand	163-165	3	9
α-helix	166-168	3
β-strand	169-170	2	9
β-strand	176-185	10	9
α-helix	186-188	3
β-strand	194-200	7	10
α-helix	201-203	3
β-strand	205-211	7	10

Chain C: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	11
β-strand	9-13	4	12
β-strand	18-24	7	11
α-helix	28-30	3
β-strand	33-38	6	12
β-strand	45-48	4	12
β-strand	49	1	13
β-strand	53	1	13
β-strand	62-67	6	11
β-strand	70-76	7	11
α-helix	80-82	3
β-strand	84-92	9	12
β-strand	95-98	4	12
β-strand	102-106	5	12
α-helix	106A	1
β-strand	111	1	14
α-helix	112-113	2
β-strand	114-118	5	15
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	15
β-strand	140	1	14
β-strand	145-150	6	16
β-strand	153-154	2	16
α-helix	155	1
β-strand	159-163	5	15
α-helix	164-167	4
β-strand	173-182	10	15
α-helix	183-186	4
β-strand	191-197	7	16
β-strand	205-210	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Suppressor of tumorigenicity 14 protein	A	protein	241	Homo sapiens	Q9Y5Y6 (AlphaFold model)
S4 FAB heavy chain	B	protein	226	Homo sapiens
S4 FAB light chain	C	protein	211	Homo sapiens

Sequence of entity 1 (A), FASTA

>3NPS_1 Suppressor of tumorigenicity 14 protein (chains A)
VVGGTDADEGEWPWQVSLHALGQGHICGASLISPNWLVSAAHCYIDDRGFRYSDPTQWTA
FLGLHDQSQRSAPGVQERRLKRIISHPFFNDFTFDYDIALLELEKPAEYSSMVRPISLPD
ASHVFPAGKAIWVTGWGHTQYGGTGALILQKGEIRVINQTTCENLLPQQITPRMMCVGFL
SGGVDSCQGDSGGPLSSVEADGRIFQAGVVSWGDGCAQRNKPGVYTRLPLFRDWIKENTG
V

Sequence of entity 2 (B), FASTA

>3NPS_2 S4 FAB HEAVY CHAIN (chains B)
EVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAGQGLEWMGGIIPIFGTANYA
QKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARTFHIRRYRSGYYDKMDHWGQGTL
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLESSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 3 (C), FASTA

>3NPS_3 S4 FAB LIGHT CHAIN (chains C)
VLTQPPSVSGAPGQRVTISCSGSSSNIGSNYVSWYQQKPGTAPKLLIYDNNQRPSGVPDR
FSGSKSGTSAVLAITGLQSEDEADYYCQSRDISQYVFGGGTKLTVLRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Primary citation

A reverse binding motif that contributes to specific protease inhibition by antibodies. Schneider, E.L., Lee, M.S., Baharuddin, A. et al. J Mol Biol (2012) 415:699-715. DOI 10.1016/j.jmb.2011.11.036 · PubMed

Other PDB entries of the same protein (UniProt Q9Y5Y6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3NCL 1.19 Å, Crystal Structure of MT-SP1 bound to Benzamidine Phosphonate Inhibitor
3P8G 1.2 Å, Crystal Structure of MT-SP1 in complex with benzamidine
8G1W 1.2 Å, Crystal Structure Matriptase (C731S) in Complex with Inhibitor VD4162B
1EAX 1.3 Å, Crystal structure of MTSP1 (matriptase)
8G1V 1.35 Å, Crystal Structure Matriptase (C731S) in Complex with Inhibitor MM1132-2
4IS5 1.48 Å, Crystal Structure of the ligand-free inactive Matriptase
6T9T 1.69 Å, Matriptase in complex with the synthetic inhibitor (S)-3-(3-(4-(3-(tert-butyl)ureido)pipe…
4JZ1 1.9 Å, Crystal Structure of Matriptase in complex with Inhibitor
4O9V 1.9 Å, Crystal structure of matriptase in complex with inhibitor
4R0I 1.9 Å, Crystal structure of matriptase in complex with inhibitor
6N4T 1.95 Å, Crystal structure of Matriptase1 in complex with a peptidomimetic benzothiazole
3P8F 2.0 Å, Crystal Structure of MT-SP1 in complex with SFTI-1

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