3BN9: MT-SP1

Crystal Structure of MT-SP1 in complex with Fab Inhibitor E2. Determined by X-ray diffraction at 2.17 Å resolution. Released 9 Sept 2008.

Method: X-ray diffraction
Resolution: 2.17 Å
Organism: Homo sapiens
Chains: 6
Atoms: 11,103
Mol. weight: 154.65 kDa
Released: 9 Sept 2008

Explore 3BN9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3BN9 contains 44 α-helices and 133 β-strands across 6 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, 24 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	19
β-strand	20-21	2	20
α-helix	22-23	2
β-strand	30-35	6	21
β-strand	39-46	8	21
β-strand	51-54	4	21
α-helix	56-59	4
β-strand	60B	1	22
β-strand	60E	1	22
α-helix	61-63	3
β-strand	64-68	5	21
β-strand	72	1	23
β-strand	81-90	10	21
β-strand	104-108	5	21
β-strand	122	1	20
α-helix	123-125	3
β-strand	135-140	6	20
β-strand	143	1	24
β-strand	151	1	24
β-strand	154	1	23
α-helix	155	1
β-strand	156-163	8	20
α-helix	165-171	7
β-strand	180-184	5	20
β-strand	189	1	19
β-strand	198-202	5	20
β-strand	207-215	9	20
β-strand	221A	1	25
β-strand	224	1	25
β-strand	227-230	4	20
α-helix	232-234	3
α-helix	235-242	8

Chain B: 7 helices, 24 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	143	1	6
β-strand	151	1	6
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
β-strand	198-202	5	2
β-strand	207-215	9	2
β-strand	221A	1	7
β-strand	224	1	7
β-strand	227-230	4	2
α-helix	232-234	3
α-helix	235-242	8

Chain C: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	8
β-strand	10-14	5	9
β-strand	19-25	7	8
β-strand	33-38	6	9
β-strand	45-49	5	9
β-strand	53-54	2	9
α-helix	55	1
β-strand	62-67	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	84-90	7	9
β-strand	97-98	2	9
β-strand	102-107	6	9
β-strand	111	1	10
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	145-150	6	12
β-strand	154	1	12
β-strand	159-163	5	11
α-helix	164-167	4
β-strand	173-182	10	11
α-helix	183-186	4
β-strand	192-197	6	12
β-strand	205-209	5	12

Chain D: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	13
β-strand	10-12	3	14
β-strand	17-25	9	13
α-helix	29-31	3
β-strand	34-39	6	14
β-strand	45-51	7	14
β-strand	57-59	3	14
α-helix	61-63	3
β-strand	67-72	6	13
β-strand	77-82A	7	13
α-helix	84-86	3
β-strand	88-95	8	14
α-helix	96	1
β-strand	100K-103	4	14
β-strand	107-111	5	14
α-helix	115-116	2
β-strand	117	1	15
β-strand	120-121	2	16
β-strand	141-145	5	16
β-strand	146	1	15
β-strand	151-154	4	17
β-strand	164-165	2	18
α-helix	166-168	3
β-strand	169-170	2	16
β-strand	176-179	4	16
β-strand	180-181	2	18
β-strand	194-200	7	17
α-helix	201-203	3
β-strand	205-211	7	17

Chain E: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	26
β-strand	10-13	4	27
β-strand	19-25	7	26
β-strand	33-38	6	27
α-helix	43-44	2
β-strand	45-49	5	27
β-strand	53-54	2	27
α-helix	55	1
β-strand	62-67	6	26
β-strand	70-75	6	26
α-helix	80-82	3
β-strand	84-90	7	27
α-helix	96	1
β-strand	97-98	2	27
β-strand	102-106	5	27
β-strand	111	1	28
β-strand	114-118	5	29
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	29
β-strand	140	1	28
β-strand	145-150	6	30
β-strand	154	1	30
β-strand	159-163	5	29
α-helix	164-167	4
β-strand	173-182	10	29
α-helix	183-186	4
β-strand	191-198	8	30
β-strand	201-210	10	30

Chain F: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	31
β-strand	10-12	3	27
β-strand	18-25	8	31
α-helix	29-31	3
β-strand	34-39	6	27
β-strand	45-51	7	27
β-strand	57-59	3	27
β-strand	67-72	6	31
β-strand	77-82	6	31
α-helix	84-86	3
β-strand	88-95	8	27
α-helix	96	1
β-strand	100K-103	4	27
β-strand	107-111	5	27
α-helix	115-116	2
β-strand	117	1	32
β-strand	120-124	5	33
β-strand	135-145	11	33
β-strand	146	1	32
β-strand	151-154	4	34
α-helix	155-157	3
β-strand	164-165	2	33
α-helix	166-168	3
β-strand	169-170	2	33
β-strand	176-185	10	33
β-strand	194-200	7	34
β-strand	205-211	7	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Membrane-type serine protease 1	A, B	protein	241	Homo sapiens	Q9Y5Y6 (AlphaFold model)
E2 Fab Light Chain	C, E	protein	214	Homo sapiens	Q6GMX0 (AlphaFold model)
E2 Fab Heavy Chain	D, F	protein	257	Homo sapiens	P01857 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3BN9_1 Membrane-type serine protease 1 (chains A, B)
VVGGTDADEGEWPWQVSLHALGQGHICGASLISPNWLVSAAHCYIDDRGFRYSDPTQWTA
FLGLHDQSQRSAPGVQERRLKRIISHPFFNDFTFDYDIALLELEKPAEYSSMVRPISLPD
ASHVFPAGKAIWVTGWGHTQYGGTGALILQKGEIRVINQTTCENLLPQQITPRMMCVGFL
SGGVDSCQGDSGGPLSSVEADGRIFQAGVVSWGDGCAQRNKPGVYTRLPLFRDWIKENTG
V

Sequence of entity 2 (C, E), FASTA

>3BN9_2 E2 Fab Light Chain (chains C, E)
DIQMTQSPSSLSASVGDRVTITCRASQGISSYLAWYQQKPGKAPKLLIYAASSLQSGVPS
RFSGSGSGTDFTLTISSLQPEDFAVYYCQQHGNLPYTFGDGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (D, F), FASTA

>3BN9_3 E2 Fab Heavy Chain (chains D, F)
QVQLVQSGGGLVKPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYY
ADSVKGRFTISRDNSKNTLYLQMSSLRAEDTAVYYCARPYLTYPQRRGPQNVSPFDNWGQ
GTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCAAAHHHHHH
GAAEQKLISEEDLNGAA

Primary citation

Structure of an Fab-protease complex reveals a highly specific non-canonical mechanism of inhibition. Farady, C.J., Egea, P.F., Schneider, E.L. et al. J Mol Biol (2008) 380:351-360. DOI 10.1016/j.jmb.2008.05.009 · 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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