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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MEMBRANE-TYPE SERINE PROTEASE 1 (MT-SP1) IN COMPLEX WITH THE FAB INHIBITOR S4

Authors :   A. Baharuddin

Date :   29 Jun 10 (Deposition) - 06 Jul 11 (Release) - 29 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Hydrolase, Antibody-Protease Complex, Protein-Protein Complex, Enzyme-Inhibitor Complex, Disease Mutation, Glycoprotein, Membrane, Serine Protease, Signal-Anchor, Transmembrane, Hydrolase - Immune System Complex, Hydrolase-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. L. Schneider, M. S. Lee, A. Baharuddin, D. H. Goetz, C. J. Farady, M. Ward, C. I. Wang, C. S. Craik
A Reverse Binding Motif That Contributes To Specific Protease Inhibition By Antibodies.
J. Mol. Biol. V. 415 699 2012
PubMed-ID: 22154938 | Reference-DOI: 10.1016/J.JMB.2011.11.036

Molecule 1 - SUPPRESSOR OF TUMORIGENICITY 14 PROTEIN
	Chains	:	A
	EC Number	:	3.4.21.109
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE30
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	PEPTIDASE S1 DOMAIN (UNP RESIDUES 615-855)
	Gene	:	PRSS14, SNC19, ST14, TADG15
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SERINE PROTEASE 14, MATRIPTASE, MEMBRANE-TYPE SERINE PROTEASE 1, MT-SP1, PROSTAMIN, SERINE PROTEASE TADG-15, TUMOR- ASSOCIATED DIFFERENTIALLY-EXPRESSED GENE 15 PROTEIN

Molecule 2 - S4 FAB HEAVY CHAIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMX7FH
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - S4 FAB LIGHT CHAIN
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMX7FH
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 16)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	EDO	10	Ligand/Ion	1,2-ETHANEDIOL
3	NA	5	Ligand/Ion	SODIUM ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:130 , ALA A:132 , ILE A:163 , GLN A:165 , ARG A:230	BINDING SITE FOR RESIDUE EDO A 1
02	AC2	SOFTWARE	GLU A:26 , TRP A:27 , HOH A:649	BINDING SITE FOR RESIDUE EDO A 2
03	AC3	SOFTWARE	ASP A:23 , GLU A:24 , GLY A:25 , GLU A:26 , TRP A:27 , PRO A:28 , LEU A:70 , HIS A:71 , LEU A:155 , HOH A:384	BINDING SITE FOR RESIDUE EDO A 3
04	AC4	SOFTWARE	HIS A:143 , HOH A:382 , GLN C:53 , HOH C:360 , HOH C:479	BINDING SITE FOR RESIDUE EDO A 4
05	AC5	SOFTWARE	HIS A:91 , PHE A:93 , PHE A:234 , TRP A:237 , HOH A:468	BINDING SITE FOR RESIDUE EDO A 6
06	AC6	SOFTWARE	HIS A:57 , CYS A:58 , ILE A:60 , TYR A:60G , ARG B:100	BINDING SITE FOR RESIDUE EDO A 7
07	AC7	SOFTWARE	ILE A:88 , SER A:90	BINDING SITE FOR RESIDUE NA A 245
08	AC8	SOFTWARE	TRP A:141 , GLY A:193	BINDING SITE FOR RESIDUE NA A 246
09	AC9	SOFTWARE	GLY B:100D , TYR B:100E , TYR B:100F , HOH B:294 , TYR C:96	BINDING SITE FOR RESIDUE EDO B 215
10	BC1	SOFTWARE	LYS B:19 , SER B:21 , TYR B:79	BINDING SITE FOR RESIDUE EDO B 216
11	BC2	SOFTWARE	HOH B:318 , THR C:5 , GLN C:6 , PRO C:7 , HOH C:395	BINDING SITE FOR RESIDUE EDO B 217
12	BC3	SOFTWARE	THR B:191 , PRO C:141 , GLN C:199 , HOH C:263 , HOH C:264 , HOH C:537	BINDING SITE FOR RESIDUE EDO C 10
13	BC4	SOFTWARE	VAL C:146 , GLU C:161 , SER C:177 , HOH C:524	BINDING SITE FOR RESIDUE NA C 213

Asymmetric/Biological Unit

No.	Residues
1	A:42	-	A:58
2	A:168	-	A:182
3	A:191	-	A:220
4	B:22	-	B:92
5	B:140	-	B:196
6	C:23	-	C:88
7	C:134	-	C:194

Asymmetric/Biological Unit

No.	Residues
1	Phe B:146	-	Pro B:147
2	Glu B:148	-	Pro B:149
3	Tyr C:140	-	Pro C:141

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_032849	G	827	R	ST14_HUMAN	Disease (ARCI11)	137852931	A	G	216	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	ST14_HUMAN	615-854	1	A:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	ST14_HUMAN	652-657	1	A:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	ST14_HUMAN	799-810	1	A:189-200

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000278742	1a	ENSE00001334626	chr11:130029457-130029955	499	ST14_HUMAN	1-27	27	0	-	-
1.2	ENST00000278742	2	ENSE00000990418	chr11:130058009-130058168	160	ST14_HUMAN	28-81	54	0	-	-
1.3	ENST00000278742	3	ENSE00000990419	chr11:130058425-130058552	128	ST14_HUMAN	81-123	43	0	-	-
1.4	ENST00000278742	4	ENSE00000990421	chr11:130058764-130058834	71	ST14_HUMAN	124-147	24	0	-	-
1.5c	ENST00000278742	5c	ENSE00000990422	chr11:130059634-130059791	158	ST14_HUMAN	147-200	54	0	-	-
1.6b	ENST00000278742	6b	ENSE00000990423	chr11:130060008-130060043	36	ST14_HUMAN	200-212	13	0	-	-
1.7b	ENST00000278742	7b	ENSE00001278516	chr11:130060349-130060589	241	ST14_HUMAN	212-292	81	0	-	-
1.8	ENST00000278742	8	ENSE00000990429	chr11:130064044-130064183	140	ST14_HUMAN	292-339	48	0	-	-
1.9	ENST00000278742	9	ENSE00000990430	chr11:130064535-130064632	98	ST14_HUMAN	339-371	33	0	-	-
1.10b	ENST00000278742	10b	ENSE00000990431	chr11:130066234-130066343	110	ST14_HUMAN	372-408	37	0	-	-
1.11b	ENST00000278742	11b	ENSE00000990432	chr11:130066465-130066595	131	ST14_HUMAN	408-452	45	0	-	-
1.12	ENST00000278742	12	ENSE00000990433	chr11:130067736-130067840	105	ST14_HUMAN	452-487	36	0	-	-
1.13	ENST00000278742	13	ENSE00000990434	chr11:130068203-130068313	111	ST14_HUMAN	487-524	38	0	-	-
1.14	ENST00000278742	14	ENSE00000990435	chr11:130068403-130068516	114	ST14_HUMAN	524-562	39	0	-	-
1.15	ENST00000278742	15	ENSE00000990436	chr11:130068842-130068964	123	ST14_HUMAN	562-603	42	0	-	-
1.16	ENST00000278742	16	ENSE00000990437	chr11:130069846-130070032	187	ST14_HUMAN	603-665	63	1	A:16-60F	51
1.17	ENST00000278742	17	ENSE00000990438	chr11:130078305-130078579	275	ST14_HUMAN	665-757	93	1	A:60F-148	93
1.18	ENST00000278742	18	ENSE00000990439	chr11:130079337-130079473	137	ST14_HUMAN	757-802	46	1	A:148-192 (gaps)	47
1.19b	ENST00000278742	19b	ENSE00000990440	chr11:130079557-130080271	715	ST14_HUMAN	803-855	53	1	A:193-244 (gaps)	54

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:241
 aligned with ST14_HUMAN | Q9Y5Y6 from UniProtKB/Swiss-Prot  Length:855

    Alignment length:241
                                   624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854 
          ST14_HUMAN    615 VVGGTDADEGEWPWQVSLHALGQGHICGASLISPNWLVSAAHCYIDDRGFRYSDPTQWTAFLGLHDQSQRSAPGVQERRLKRIISHPFFNDFTFDYDIALLELEKPAEYSSMVRPICLPDASHVFPAGKAIWVTGWGHTQYGGTGALILQKGEIRVINQTTCENLLPQQITPRMMCVGFLSGGVDSCQGDSGGPLSSVEADGRIFQAGVVSWGDGCAQRNKPGVYTRLPLFRDWIKENTGV  855
               SCOP domains d3npsa_ A: Matriptase MTSP1                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Trypsin-3npsA01 A:16-238                                                                                                                                                                                                                   ------ Pfam domains
         Sec.struct. author ....ee........eeeeee...eeeeeeee....eeeehhhhhh........hhh.eeeee.............eeeeeeeeee.............eeeee..........................eeeeee..............eeeeeee.hhhhhhhhh.......eeeee...............eeeee.....eeeeeeeee..........eeeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R---------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 615-854                                                                                                                                                                                                     - PROSITE (1)
                PROSITE (2) -------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.16  PDB: A:16-60F UniProt: 603-665          -------------------------------------------------------------------------------------------Exon 1.18  PDB: A:148-192 (gaps)              Exon 1.19b  PDB: A:193-244 (gaps) UniProt: 803-855    Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------Exon 1.17  PDB: A:60F-148 UniProt: 665-757                                                   -------------------------------------------------------------------------------------------------- Transcript 1 (2)
                3nps A   16 VVGGTDADEGEWPWQVSLHALGQGHICGASLISPNWLVSAAHCYIDDRGFRYSDPTQWTAFLGLHDQSQRSAPGVQERRLKRIISHPFFNDFTFDYDIALLELEKPAEYSSMVRPISLPDASHVFPAGKAIWVTGWGHTQYGGTGALILQKGEIRVINQTTCENLLPQQITPRMMCVGFLSGGVDSCQGDSGGPLSSVEADGRIFQAGVVSWGDGCAQRNKPGVYTRLPLFRDWIKENTGV  244
                                    25        35        45        55     ||60E||||    66        76 |      85        95       105       115       125       135       145  ||   156       166       176       185 |     194       204|      213   ||  223       233       243 
                                                                       60A||||||||               77A                                                                    148|                               184A  |               204A          217|  |                       
                                                                        60B|||||||                                                                                       150                                  186A                              219  |                       
                                                                         60C||||||                                                                                                                                                                221A                       
                                                                          60D|||||                                                                                                                                                                                           
                                                                           60E||||                                                                                                                                                                                           
                                                                            60F|||                                                                                                                                                                                           
                                                                             60G||                                                                                                                                                                                           
                                                                              60H|                                                                                                                                                                                           
                                                                               60I

Chain B from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eee.....eeeeeee.......eeeeeeee....eeeeeee.......ee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeeee...........eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3nps B    1 EVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAGQGLEWMGGIIPIFGTANYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARTFHIRRYRSGYYDKMDHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLESSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        41        51 |      60        70        80  |||   87        97   |||100G||     108       118       128       138       148       158       168       178       188       198       208      
                                                                 39|         52A                            82A||               100A||||||||                                                                                                                  
                                                                  41                                         82B|                100B|||||||                                                                                                                  
                                                                                                              82C                 100C||||||                                                                                                                  
                                                                                                                                   100D|||||                                                                                                                  
                                                                                                                                    100E||||                                                                                                                  
                                                                                                                                     100F|||                                                                                                                  
                                                                                                                                      100G||                                                                                                                  
                                                                                                                                       100H|                                                                                                                  
                                                                                                                                        100I

Chain C from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains d3npsc1 C:3-106A automated matches                                                                        d3npsc2 C:108-212 automated matches                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee....eeeeeee....hhhhh.eeeeee......eeee.............eeeeee..eeeeeee..hhhhheeeeeeeee..eeee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3nps C    3 VLTQPPSVSGAPGQRVTISCSGSSSNIGSNYVSWYQQKPGTAPKLLIYDNNQRPSGVPDRFSGSKSGTSAVLAITGLQSEDEADYYCQSRDISQYVFGGGTKLTVLRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                  ||13        23    ||  31        41        51        61        71        81        91       101     ||111       121       131       141       151       161       171       181       191       201       211 
                                  9|              27A|                                                                            106A|                                                                                                        
                                  11               27B                                                                              108

Legend:		→ Mismatch	(orange background)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "CATH Domain" information available for 3NPS)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Homo sapiens (Human) (339)

Trypsin-3npsA01

A:16-238

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ST14_HUMAN | Q9Y5Y6)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0060672	epithelial cell morphogenesis involved in placental branching	The change in form (cell shape and size) that occurs when a trophoblast cell elongates to contribute to the branching of the placenta.
	GO:0030216	keratinocyte differentiation	The process in which a relatively unspecialized cell acquires specialized features of a keratinocyte.
	GO:0001843	neural tube closure	The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0016323	basolateral plasma membrane	The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0019897	extrinsic component of plasma membrane	The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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		Tyr C:140 - Pro C:141	[ RasMol ]

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	3nps
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(no "Related Entries Specified in the PDB File" available for 3NPS)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 16)

Sites (13, 13)

SS Bonds (7, 7)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (3, 3)

Exons (4, 4)

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