2R0K - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   PROTEASE DOMAIN OF HGFA WITH INHIBITOR FAB58

Authors :   C. Eigenbrot, S. Shia

Date :   20 Aug 07 (Deposition) - 25 Dec 07 (Release) - 05 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.51

Chains :   Asym./Biol. Unit : A,H,L

Keywords :   Serine Protease, Antibody, Inhibitor, Egf-Like Domain, Glycoprotein, Hydrolase, Kringle, Secreted, Zymogen, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Wu, C. Eigenbrot, W. C. Liang, S. Stawicki, S. Shia, B. Fan, R. Ganesan, M. T. Lipari, D. Kirchhofer
Structural Insight Into Distinct Mechanisms Of Protease Inhibition By Antibodies.
Proc. Natl. Acad. Sci. Usa V. 104 19784 2007
PubMed-ID: 18077410 | Reference-DOI: 10.1073/PNAS.0708251104

Molecule 1 - HEPATOCYTE GROWTH FACTOR ACTIVATOR
	Chains	:	A
	EC Number	:	3.4.21.-
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Expression System Vector Type	:	VIRUS
	Fragment	:	HGFA PROTEASE DOMAIN
	Gene	:	HGFAC
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - ANTIBODY LIGHT CHAIN OF FAB58
	Chains	:	L
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	THE PROTEIN WAS MADE USING A SYNTHETICALLY DIVERSIFIED GENE LIBRARY AND SELECTED FOR TIGHT BINDING TO A SPECIFIC TARGET ON A PLASTIC SURFACE. THE GENE LIBRARY USED CLONED HUMAN GENES AS ITS BASIS

Molecule 3 - ANTIBODY HEAVY CHAIN OF FAB58, FAB PORTION ONLY
	Chains	:	H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	THE PROTEIN WAS MADE USING A SYNTHETICALLY DIVERSIFIED GENE LIBRARY AND SELECTED FOR TIGHT BINDING TO A SPECIFIC TARGET ON A PLASTIC SURFACE. THE GENE LIBRARY USED CLONED HUMAN GENES AS ITS BASIS.

		1	2	3
Asymmetric/Biological Unit	:	A	H	L

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2R0K)

(no "Site" information available for 2R0K)

Asymmetric/Biological Unit

No.	Residues
1	A:42	-	A:58
2	A:50	-	A:111D
3	A:136	-	A:201
4	A:168	-	A:182
5	A:191	-	A:220
6	H:22	-	H:92
7	H:140	-	H:196
8	L:23	-	L:88
9	L:134	-	L:194
10	L:214	-	H:216

Asymmetric/Biological Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	Thr L:94	-	Pro L:95
3	Tyr L:140	-	Pro L:141
4	Phe H:146	-	Pro H:147
5	Glu H:148	-	Pro H:149
6	Ser H:153	-	Trp H:154
7	Asn H:155	-	Ser H:156

Asymmetric/Biological Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024295	R	644	Q	HGFA_HUMAN	Polymorphism	2498323	A	R	241	Q
2	UniProt	VAR_024294	R	509	H	HGFA_HUMAN	Polymorphism	16844401	A	R	111C	H

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.	HGFA_HUMAN	408-646	1	A:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	HGFA_HUMAN	443-448	1	A:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	HGFA_HUMAN	592-603	1	A:189-200

Asymmetric/Biological Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000382774	1a	ENSE00001493344	chr4:3443614-3443845	232	HGFA_HUMAN	1-39	39	0	-	-
1.2	ENST00000382774	2	ENSE00000699356	chr4:3444459-3444639	181	HGFA_HUMAN	40-100	61	0	-	-
1.3	ENST00000382774	3	ENSE00000699357	chr4:3444777-3444873	97	HGFA_HUMAN	100-132	33	0	-	-
1.4	ENST00000382774	4	ENSE00000699358	chr4:3445068-3445147	80	HGFA_HUMAN	132-159	28	0	-	-
1.5	ENST00000382774	5	ENSE00000699359	chr4:3445766-3445888	123	HGFA_HUMAN	159-200	42	0	-	-
1.6a	ENST00000382774	6a	ENSE00000699360	chr4:3446038-3446169	132	HGFA_HUMAN	200-244	45	0	-	-
1.7	ENST00000382774	7	ENSE00001267259	chr4:3446350-3446460	111	HGFA_HUMAN	244-281	38	0	-	-
1.8	ENST00000382774	8	ENSE00001267254	chr4:3446546-3446720	175	HGFA_HUMAN	281-339	59	0	-	-
1.9a	ENST00000382774	9a	ENSE00000699364	chr4:3446992-3447077	86	HGFA_HUMAN	339-368	30	0	-	-
1.10b	ENST00000382774	10b	ENSE00000699365	chr4:3447769-3448021	253	HGFA_HUMAN	368-452	85	1	A:16-60B (gaps)	47
1.11	ENST00000382774	11	ENSE00000699367	chr4:3449219-3449358	140	HGFA_HUMAN	452-499	48	1	A:60B-104	48
1.12	ENST00000382774	12	ENSE00000699371	chr4:3449622-3449762	141	HGFA_HUMAN	499-546	48	1	A:104-147	48
1.13b	ENST00000382774	13b	ENSE00000699372	chr4:3449855-3450003	149	HGFA_HUMAN	546-595	50	1	A:147-192	50
1.14c	ENST00000382774	14c	ENSE00001493333	chr4:3450964-3451211	248	HGFA_HUMAN	596-655	60	1	A:193-243 (gaps)	52

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:239
 aligned with HGFA_HUMAN | Q04756 from UniProtKB/Swiss-Prot  Length:655

    Alignment length:239
                                   417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637         
          HGFA_HUMAN    408 IIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRIR  646
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2r0kA01     2r0kA02 A:28-120,A:231-243 Trypsin-like serine proteases                                            2r0kA01 A:16-27,A:121-230 Trypsin-like serine proteases                                                           2r0kA02       CATH domains
               Pfam domains Trypsin-2r0kA01 A:16-238                                                                                                                                                                                                                  ----- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeee....eeeehhhhh....hhh.eeeee............eee.eeeeee..............eeeee..............................eeeeee...............eeeeee..hhhhhhh...hhhhh.....ee................eeeeee..eeeeeeeeee..........eeeee...hhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------H--------------------------------------------------------------------------------------------------------------------------------------Q-- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 408-646                                                                                                                                                                                                     PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI-----------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.10b  PDB: A:16-60B (gaps) [INCOMPLETE]----------------------------------------------Exon 1.12  PDB: A:104-147 UniProt: 499-546      -------------------------------------------------Exon 1.14c  PDB: A:193-243 (gaps) UniProt: 596-655  Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.11  PDB: A:60B-104 UniProt: 452-499      ----------------------------------------------Exon 1.13b  PDB: A:147-192 UniProt: 546-595       --------------------------------------------------- Transcript 1 (2)
                2r0k A   16 IIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRIR  243
                                    25        35||      47        57   |||| 63        73        83        93     | 102      111A|||    118       128       138       148       158       168  ||   176       185   |   194       204       214  || | 224       234         
                                               36|                   60A|||                                    99A          111A|||                                                        170A|          184A  188A                          217| |                       
                                                39                    60B||                                                  111B||                                                         170B                                               219 |                       
                                                                       60C|                                                   111C|                                                                                                             221A                       
                                                                        60D                                                    111D

Chain H from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d2r0kh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                       d2r0kh2 H:114-212 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma             ---- SCOP domains
               CATH domains 2r0kH01 H:1-113 Immunoglobulins                                                                                      2r0kH02 H:114-216 Immunoglobulins                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee....eeeeeeeee.......eeeeeee.....eeeeeeee....eeee.......eeeeee....eeeeeee..hhhhheeeeeeee....eeee...eeeee...........ee...eeeeee..eee.....eeee........eee...eee...eee..eeeeee........eeeeeeehhhheeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2r0k H    1 EVQLVESGGGLVQPGGSLRLSCAASGFTITGSAIHWVRQAPGKGLEWVAIINPNGGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSARFSFDYWGQGTLVTVSSASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126|      143       153       163       173       183       193       203       213   
                                                                              52A                            82A||                                         126|                                                                                  
                                                                                                              82B|                                          134                                                                                  
                                                                                                               82C

Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2r0kL01 L:1-108 Immunoglobulins                                                                             2r0kL02 L:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhheeeeeee............eeeee......eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..ee......eee.........eeeeeeeeehhhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2r0k L    1 DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYTTPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Thrombin, subunit H (1535)

Homologous Superfamily: Trypsin-like serine proteases (1488)

Human (Homo sapiens) (615)

1a	2r0kA01	A:16-27,A:121-230
1b	2r0kA02	A:28-120,A:231-243

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

2a	2r0kL02	L:109-214
2b	2r0kH02	H:114-216
2c	2r0kH01	H:1-113
2d	2r0kL01	L:1-108

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Homo sapiens (Human) (339)

Trypsin-2r0kA01

A:16-238

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (HGFA_HUMAN | Q04756)

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:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	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.

Asymmetric/Biological Unit
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(no "Sites" information available for 2r0k)

	Cis Peptide Bonds
		Asn H:155 - Ser H:156	[ RasMol ]
		Glu H:148 - Pro H:149	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Ser H:153 - Trp H:154	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Thr L:94 - Pro L:95	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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	2r0k
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	HGFA_HUMAN \| Q04756
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	3.4.21.-
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UniProtKB/Swiss-Prot
	HGFA_HUMAN \| Q04756	:	1ybw 1yc0 2r0l 2wub 2wuc 3k2u

1ybw	PROTEASE DOMAIN OF HGFA WITH NO INHIBITOR
1yc0	SHORT FORM HGFA WITH KUNITZ DOMAIN 1 FROM HAI-1
2r0l

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (10, 10)

Cis Peptide Bonds (7, 7)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (3, 3)

Exons (5, 5)

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