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Asym./Biol. Unit (Jmol Viewer)

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

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

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

Date :   01 Oct 09 (Deposition) - 15 Dec 09 (Release) - 21 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Serine Protease, Egf-Like Domain, Allosteric Inhibitor, Kringle, Antibody, Hydrolase, Fab Complex, Glycoprotein, Immune System, Hydrolase-Hydrolase Inhibitor Complex (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
	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
	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
	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 - ACE-KQLR-CHLOROMETHYLKETONE INHIBITOR
	Chains	:	I
	Engineered	:	YES
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

Molecule 5 - FAB FRAGMENT FAB40.DELTATRP LIGHT CHAIN
	Chains	:	L
	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
Asymmetric/Biological Unit	:	A	B	H	I	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 5)

No.	Name	Count	Type	Full Name
1	0QE	1	Mod. Amino Acid	CHLOROMETHANE
2	ACE	1	Mod. Amino Acid	ACETYL GROUP
3	AR7	1	Mod. Amino Acid	AMINO{[(4S)-4-AMINO-5,5-DIHYDROXYPENTYL]AMINO}METHANIMINIUM
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:74	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 74 RESIDUES 1244 TO 1245
2	AC2	SOFTWARE	HIS A:57 , SER A:99 , PRO A:99A , LYS A:110 , LYS A:111 , GLY A:111A , ASP A:175 , ASP A:189 , ALA A:190 , CYS A:191 , GLN A:192 , GLY A:193 , SER A:195 , SER A:214 , TRP A:215 , GLY A:216 , ASP A:217 , GLY A:219 , HOH A:2027 , 0QE I:6 , HOH I:2001 , HOH I:2002	BINDING SITE FOR CHAIN I OF ACE-KQLR- CHLOROMETHYLKETONE INHIBITOR

Asymmetric/Biological 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	H:22	-	H:92
8	H:140	-	H:196
9	H:216	-	L:214
10	L:23	-	L:88
11	L:134	-	L:194

Asymmetric/Biological 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

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, 6)

	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	2	A:16-60B (gaps) B:392-398	47 7
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:193-244 (gaps) -	53 -

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:240
 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 2wucA01     2wucA02 A:28-120,A:231-244 Trypsin-like serine proteases                                            2wucA01 A:16-27,A:121-230 Trypsin-like serine proteases                                                           2wucA02        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeee..eeeehhhhh....hhh.eeeee............eeeeeeeeee..............eeeee..............................eeeeee...............eeeeee..hhhhhh....hhhhh...eeee................eeeeee..eeeeeeeeee..........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 UniProt: 546-595       ---------------------------------------------------- Transcript 1 (2)
                2wuc A   16 IIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLDENVSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISWGDGCGRLHKPGVYTRVANYVDWINDRIRP  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  188A                          217| |                        
                                                39                    60B||                                                  111B||                                                         170B                                               219 |                        
                                                                       60C|                                                   111C|                                                                                                             221A                        
                                                                        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)
                2wuc B  392 ACGRRHK  398

Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wucH01 H:1-113 Immunoglobulins                                                                                      2wucH02 H:114-217 Immunoglobulins                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee.......eeeeeee......eeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeee..ee...........eeeee........eeeee........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee........eeeeeeehhhheeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2wuc H    1 EVQLVESGGGLVQPGGSLRLSCAASGFTINGTYIHWVRQAPGKGLEWVGGIYPAGGATYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCAKWAWPAFDYWGQGTLVTVSSASTKGPSVFPLAPSSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD  217
                                    10        20        30        40        50  |     59        69        79   |||  86        97  |    106       116       126 ||    138       148       158       168       178       188       198       208         
                                                                              52A                            82A||           95|  |                          128|                                                                                      
                                                                                                              82B|            97  |                           131                                                                                      
                                                                                                               82C             100A

Chain I from PDB  Type:PROTEIN  Length:6
                                       
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                2wuc I    1 xKQLrx    6
                            |   ||
                            1-ACE|
                                5-AR7
                                 6-0QE

Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d2wucl1 L:1-107 automated matches                                                                          d2wucl2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------2wucL02 L:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee.....hhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2wuc 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

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(

)

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)

d2wucl1

L:1-107

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

Protein domain: automated matches (652)

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

d2wucl2

L:108-214

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	2wucA01	A:16-27,A:121-230
1b	2wucA02	A:28-120,A:231-244

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

2a	2wucL02	L:109-214
2b	2wucH02	H:114-217
2c	2wucH01	H:1-113

(no "Pfam Domain" information available for 2WUC)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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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	Cis Peptide Bonds
		Ala L:94 - Pro L:95	[ RasMol ]
		Glu H:148 - Pro H:149	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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Access by PDB/NDB ID
	2wuc
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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 2wub 3k2u

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (2, 2)

SS Bonds (11, 11)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (3, 3)

Exons (5, 6)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (2, 5)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File