3SO3: Suppressor of tumorigenicity 14 protein

Structures of Fab-Protease Complexes Reveal a Highly Specific Non-Canonical Mechanism of Inhibition. Determined by X-ray diffraction at 2.1 Å resolution. Released 20 Jun 2012.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,605
Mol. weight: 74.33 kDa
Released: 20 Jun 2012

Explore 3SO3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3SO3 contains 30 α-helices and 67 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: 11 helices, 22 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
α-helix	111-114	4
α-helix	120-121	2
β-strand	122	1	2
α-helix	123-125	3
β-strand	135-140	6	2
β-strand	143	1	6
β-strand	151	1	6
β-strand	154	1	5
β-strand	156-162	7	2
α-helix	163-164	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: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
α-helix	17-18	2
β-strand	19-28	11	7
α-helix	30-32	3
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-75	14	7
α-helix	80-82	3
β-strand	84-93	10	8
β-strand	95A-98	5	8
β-strand	102-106	5	8
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-154	2	11
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-186	4
β-strand	191-197	7	11
β-strand	205-210	6	11

Chain C: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	34-39	6	13
β-strand	45-51	7	13
β-strand	57-59	3	13
β-strand	67-72	6	12
β-strand	77-82	6	12
α-helix	84-86	3
β-strand	88-95	8	13
β-strand	98	1	14
α-helix	99-100A	3
β-strand	100C	1	14
β-strand	100H-103	4	13
β-strand	107-111	5	13
α-helix	115-116	2
β-strand	117	1	15
α-helix	118-119	2
β-strand	120-124	5	16
α-helix	125-127	3
β-strand	135-145	11	16
β-strand	146	1	15
β-strand	151-154	4	17
α-helix	155-157	3
β-strand	163-165	3	16
α-helix	166-168	3
β-strand	169-170	2	16
β-strand	176-185	10	16
α-helix	186-188	3
β-strand	189	1	18
β-strand	192	1	18
β-strand	195-200	6	17
α-helix	201-203	3
β-strand	205-210	6	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Suppressor of tumorigenicity 14 protein	A	protein	241	Homo sapiens	Q9Y5Y6 (AlphaFold model)
A11 FAB light chain	B	protein	217	Homo sapiens
A11 FAB heavy chain	C	protein	228	Homo sapiens

Sequence of entity 1 (A), FASTA

>3SO3_1 Suppressor of tumorigenicity 14 protein (chains A)
VVGGTDADEGEWPWQVSLHALGQGHICGASLISPNWLVSAAHCYIDDRGFRYSDPTQWTA
FLGLHDQSQRSAPGVQERRLKRIISHPFFNDFTFDYDIALLELEKPAEYSSMVRPISLPD
ASHVFPAGKAIWVTGWGHTQYGGTGALILQKGEIRVINQTTCENLLPQQITPRMMCVGFL
SGGVDSCQGDSGGPLSSVEADGRIFQAGVVSWGDGCAQRNKPGVYTRLPLFRDWIKENTG
V

Sequence of entity 2 (B), FASTA

>3SO3_2 A11 FAB light chain (chains B)
EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASTRATGIP
ARFSGSGSGTDFTLTINSLEPEDFAVYYCQQRSNWPPGYTFGQGTKVEITRTVAAPSVFI
FPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C), FASTA

>3SO3_3 A11 FAB heavy chain (chains C)
EVQLVQSGGGLVKPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYY
ADSVKGRFTISRDNSKNTLYLQMSSLRAEDTAVYYCVKDLGIAARRFVSGAFDIWGQGTM
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDTKVEPKSC

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
3NPS 1.5 Å, Crystal structure of membrane-type serine protease 1 (MT-SP1) in complex with the Fab…
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

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