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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HGFA IN COMPLEX WITH THE ALLOSTERIC NON-INHIBITORY ANTIBODY FAB40.DELTATRP

Authors :   R. Ganesan, C. Eigenbrot, S. Shia

Date :   01 Oct 09 (Deposition) - 15 Dec 09 (Release) - 28 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A,B,C,D,H,L,Q,R
Biol. Unit 1: C,D,Q,R  (1x)
Biol. Unit 2: A,B,H,L  (1x)

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

Reference :   R. Ganesan, C. Eigenbrot, Y. Wu, W. C. Liang, S. Shia, M. T. Lipari, D. Kirchhofer
Unraveling The Allosteric Mechanism Of Serine Protease Inhibition By An Antibody
Structure V. 17 1614 2009
PubMed-ID: 20004165 | Reference-DOI: 10.1016/J.STR.2009.09.014

Molecule 1 - HEPATOCYTE GROWTH FACTOR ACTIVATOR LONG CHAIN
	Chains	:	A, C
	EC Number	:	3.4.21.-
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Common	:	CABBAGE LOOPER
	Expression System Taxid	:	7111
	Expression System Vector	:	BACULOGOLD
	Expression System Vector Type	:	BACULOVIRUS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	N-GLYCOSYLATION AT ASN74

Molecule 2 - HEPATOCYTE GROWTH FACTOR ACTIVATOR SHORT CHAIN
	Chains	:	B, D
	EC Number	:	3.4.21.-
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Common	:	CABBAGE LOOPER
	Expression System Taxid	:	7111
	Expression System Vector	:	BACULOGOLD
	Expression System Vector Type	:	BACULOVIRUS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - FAB FRAGMENT FAB40.DELTATRP HEAVY CHAIN
	Chains	:	H, R
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	33D3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 4 - FAB FRAGMENT FAB40.DELTATRP LIGHT CHAIN
	Chains	:	L, Q
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	33D3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	H	L	Q	R
Biological Unit 1 (1x)	:			C	D			Q	R
Biological Unit 2 (1x)	:	A	B			H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:74 , HOH A:2022 , HOH A:2023 , HOH A:2024	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 74 RESIDUES 1245 TO 1247
2	AC2	SOFTWARE	ASN C:74 , HOH C:2023	BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 74 RESIDUES 1245 TO 1247

Asymmetric Unit

No.	Residues
1	A:42	-	A:58
2	A:50	-	A:111D
3	A:122	-	B:393
4	A:136	-	A:201
5	A:168	-	A:182
6	A:191	-	A:220
7	C:42	-	C:58
8	C:50	-	C:111D
9	C:122	-	D:393
10	C:136	-	C:201
11	C:168	-	C:182
12	C:191	-	C:220
13	H:22	-	H:92
14	H:140	-	H:196
15	H:216	-	L:214
16	L:23	-	L:88
17	L:134	-	L:194
18	Q:23	-	Q:88
19	Q:134	-	Q:194
20	R:22	-	R:92
21	R:140	-	R:196

Asymmetric Unit

No.	Residues
1	Phe H:146	-	Pro H:147
2	Glu H:148	-	Pro H:149
3	Ser L:7	-	Pro L:8
4	Ala L:94	-	Pro L:95
5	Tyr L:140	-	Pro L:141
6	Ser Q:7	-	Pro Q:8
7	Ala Q:94	-	Pro Q:95
8	Tyr Q:140	-	Pro Q:141
9	Phe R:146	-	Pro R:147
10	Glu R:148	-	Pro R:149

Asymmetric Unit (2, 4)

								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/C	R	241	Q
2	UniProt	VAR_024294	R	509	H	HGFA_HUMAN	Polymorphism	16844401	A/C	R	111C	H

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

Biological Unit 1 (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	C	R	241	Q
2	UniProt	VAR_024294	R	509	H	HGFA_HUMAN	Polymorphism	16844401	C	R	111C	H

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

Biological Unit 2 (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 Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	HGFA_HUMAN	408-646	2	A:16-243 C:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	HGFA_HUMAN	443-448	2	A:53-58 C:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	HGFA_HUMAN	592-603	2	A:190-200 C:189-200

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

Biological Unit 2 (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:190-200 -

Asymmetric Unit (5, 12)

	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	4	A:16-60B (gaps) B:392-398 C:16-60B (gaps) D:392-397	47 7 47 6
1.11	ENST00000382774	11	ENSE00000699367	chr4:3449219-3449358	140	HGFA_HUMAN	452-499	48	2	A:60B-104 - C:60B-104 -	48 - 48 -
1.12	ENST00000382774	12	ENSE00000699371	chr4:3449622-3449762	141	HGFA_HUMAN	499-546	48	2	A:104-147 - C:104-143 -	48 - 44 -
1.13b	ENST00000382774	13b	ENSE00000699372	chr4:3449855-3450003	149	HGFA_HUMAN	546-595	50	2	A:147-192 (gaps) - C:152-192 -	50 - 45 -
1.14c	ENST00000382774	14c	ENSE00001493333	chr4:3450964-3451211	248	HGFA_HUMAN	596-655	60	2	A:193-244 (gaps) - C:193-244 (gaps) -	53 - 52 -

Asymmetric 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:232
 aligned with HGFA_HUMAN | Q04756 from UniProtKB/Swiss-Prot  Length:655

    Alignment length:240
                                   417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647
          HGFA_HUMAN    408 IIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRIRP  647
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2wubA01     2wubA02 A:28-120,A:231-244 Trypsin-like serine proteases                                            2wubA01 A:16-27,A:121-230 Trypsin-like serine proteases                                                           2wubA02        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeeee..eeeeeeeee..eeeehhhhh....hhh.eeeee............eeeeeeeeee..............eeeee..............................eeeeee...............eeeeeeeehhhhhh............eeee.....---........eeeeee..eeeeeeee...--..---..eeee.hhhhhhhhhhhhh. 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:193-244 (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 (gaps) UniProt: 546-595---------------------------------------------------- Transcript 1 (2)
                2wub A   16 IIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDC---ACQGDSGGPLACEKNGVAYLYGIISWG--CG---KPGVYTRVANYVDWINDRIRP  244
                                    25        35||      47        57   |||| 63        73        83        93     | 102      111A|||    118       128       138       148       158       168  ||   176       185 |   | 194       204       214 |  || 224       234       244
                                               36|                   60A|||                                    99A          111A|||                                                        170A|          184A 187 190                       216  || 224                    
                                                39                    60B||                                                  111B||                                                         170B                                                220|                        
                                                                       60C|                                                   111C|                                                                                                              221                        
                                                                        60D                                                    111D

Chain B from PDB  Type:PROTEIN  Length:7
 aligned with HGFA_HUMAN | Q04756 from UniProtKB/Swiss-Prot  Length:655

    Alignment length:7
          HGFA_HUMAN    393 ACGRRHK  399
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                PROSITE (1) ------- PROSITE (1)
                PROSITE (2) ------- PROSITE (2)
           Transcript 1 (1) 1.10b   Transcript 1 (1)
           Transcript 1 (2) ------- Transcript 1 (2)
                2wub B  392 ACGRRHK  398

Chain C from PDB  Type:PROTEIN  Length:229
 aligned with HGFA_HUMAN | Q04756 from UniProtKB/Swiss-Prot  Length:655

    Alignment length:240
                                   417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647
          HGFA_HUMAN    408 IIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRIRP  647
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2wubC01     2wubC02 C:28-120,C:231-244 Trypsin-like serine proteases                                            2wubC01 C:16-27,C:121-2        30 Trypsin-like serine proteases                                                   2wubC02        CATH domains
           Pfam domains (1) Trypsin-2wubC01 C:16-238                                                                                                                                                                                                                  ------ Pfam domains (1)
           Pfam domains (2) Trypsin-2wubC02 C:16-238                                                                                                                                                                                                                  ------ Pfam domains (2)
         Sec.struct. author ..............eeeeee..eeeeeeeee..eeeehhhhh....hhh.eeeee............eeeeeeeeee..............eeeee..............................eeeeee...--------....eeeeee..hhhhhh............eeee................eeeeee..eeeeeeee...---......eeeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------H--------------------------------------------------------------------------------------------------------------------------------------Q--- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: C:16-243 UniProt: 408-646                                                                                                                                                                                                    - PROSITE (1)
                PROSITE (2) -----------------------------------TRYPSI-----------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.10b  PDB: C:16-60B (gaps) [INCOMPLETE]----------------------------------------------Exon 1.12  PDB: C:104-143 UniProt: 499-546      -------------------------------------------------Exon 1.14c  PDB: C:193-244 (gaps) UniProt: 596-655   Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.11  PDB: C:60B-104 UniProt: 452-499      ----------------------------------------------Exon 1.13b  PDB: C:152-192 UniProt: 546-595       ---------------------------------------------------- Transcript 1 (2)
                2wub C   16 IIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGH--------SSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWG---CRLHKPGVYTRVANYVDWINDRIRP  244
                                    25        35||      47        57   |||| 63        73        83        93      |102      111A|||    118       128       138    |    -   |   158       168  ||   176       185   |   194       204       214 |   | 224       234       244
                                               36|                   60A|||                                     99A         111A|||                             143      152               170A|          184A  188A                         216 220                        
                                                39                    60B||                                                  111B||                                                         170B                                                                            
                                                                       60C|                                                   111C|                                                                                                                                         
                                                                        60D                                                    111D

Chain D from PDB  Type:PROTEIN  Length:6
 aligned with HGFA_HUMAN | Q04756 from UniProtKB/Swiss-Prot  Length:655

    Alignment length:6
          HGFA_HUMAN    393 ACGRRH  398
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                PROSITE (1) ------ PROSITE (1)
                PROSITE (2) ------ PROSITE (2)
           Transcript 1 (1) 1.10b  Transcript 1 (1)
           Transcript 1 (2) ------ Transcript 1 (2)
                2wub D  392 ACGRRH  397

Chain H from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wubH01 H:1-113 Immunoglobulins                                                                                      2wubH02 H:114-217 Immunoglobulins                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeeee....eeee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee............eeeee........eeeee....eeeeeeeeee.....eeee.hhh....eee..........eeeeeeeeehhhhhh...eeeeeeehhhheeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2wub H    1 EVQLVESGGGLVQPGGSLRLSCAASGFTINGTYIHWVRQAPGKGLEWVGGIYPAGGATYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCAKWAWPAFDYWGQGTLVTVSSASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD  217
                                    10        20        30        40        50  |     59        69        79   |||  86        97  |    106       116       126|      143       153       163       173       183       193       203       213    
                                                                              52A                            82A||           95|  |                        126|                                                                                   
                                                                                                              82B|            97  |                         134                                                                                   
                                                                                                               82C             100A

Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d2wubl1 L:1-107 automated matches                                                                          d2wubl2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------2wubL02 L:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2wub L    1 DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSNRAPATFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain Q from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d2wubq1 Q:1-107 automated matches                                                                          d2wubq2 Q:108-214 automated matches                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------2wubQ02 Q:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2wub Q    1 DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSNRAPATFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain R from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wubR01 R:1-113 Immunoglobulins                                                                                      2wubR02 R:114-209 Immunoglobulins                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee....eeee...eeeee........eeee.....eeeeeeeeee.....eeee.hhh....eee..........eeeeeeeee.hhhhh.....eeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2wub R    1 EVQLVESGGGLVQPGGSLRLSCAASGFTINGTYIHWVRQAPGKGLEWVGGIYPAGGATYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCAKWAWPAFDYWGQGTLVTVSSASTKGPSVFPLAPGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDK  209
                                    10        20        30        40        50  |     59        69        79   |||  86        97  |    106       116       126|      143       153       163       173       183       193       203      
                                                                              52A                            82A||           95|  |                        126|                                                                           
                                                                                                              82B|            97  |                         134                                                                           
                                                                                                               82C             100A

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Human (Homo sapiens) [TaxId: 9606] (448)

1a	d2wubl1	L:1-107
1b	d2wubq1	Q:1-107

Family: C1 set domains (antibody constant domain-like) (3013)

Protein domain: automated matches (652)

Human (Homo sapiens) [TaxId: 9606] (334)

2a	d2wubl2	L:108-214
2b	d2wubq2	Q:108-214

Asymmetric 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	2wubC01	C:16-27,C:121-230
1b	2wubA01	A:16-27,A:121-230
1c	2wubA02	A:28-120,A:231-244
1d	2wubC02	C:28-120,C:231-244

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

2a	2wubL02	L:109-214
2b	2wubH02	H:114-217
2c	2wubR02	R:114-209
2d	2wubH01	H:1-113
2e	2wubR01	R:1-113
2f	2wubQ02	Q:109-214

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Homo sapiens (Human) (339)

1a	Trypsin-2wubC01	C:16-238
1b	Trypsin-2wubC02	C:16-238

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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 Unit
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Access by PDB/NDB ID
	2wub
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	HGFA_HUMAN \| Q04756
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	3.4.21.-
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	HGFA_HUMAN \| Q04756
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UniProtKB/Swiss-Prot
	HGFA_HUMAN \| Q04756	:	1ybw 1yc0 2r0k 2r0l 2wuc 3k2u

1ybw	PROTEASE DOMAIN OF HGFA WITH NO INHIBITOR
1yc0	SHORT FORM HGFA WITH FIRST KUNITZ DOMAIN FROM HAI-1
2wuc	CRYSTAL STRUCTURE OF HGFA IN COMPLEX WITH THE ALLOSTERIC NON-INHIBITORY ANTIBODY FAB40. DELTATRP AND AC-KQLR-CHLOROMETHYLKETONE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (2, 2)

SS Bonds (21, 21)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

PROSITE Motifs (3, 6)

Exons (5, 12)

Sequences/Alignments

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SCOP Domains (2, 4)

CATH Domains (2, 10)

Pfam Domains (1, 2)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File