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(-) Description

Title :  SHORT FORM HGFA WITH INHIBITORY FAB75
 
Authors :  C. Eigenbrot, S. Shia
Date :  20 Aug 07  (Deposition) - 25 Dec 07  (Release) - 25 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,H,L
Keywords :  Serine Protease, Antibody, Allosteric 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

(-) Compounds

Molecule 1 - ANTIBODY LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS, SYNTHETIC CONSTRUCT
    Organism Taxid: 9606, 32630
    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 2 - ANTIBODY HEAVY CHAIN, FAB PORTION ONLY
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS, SYNTHETIC CONSTRUCT
    Organism Taxid: 9606, 32630
    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 - 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: SHORT FORM HGFA
    Gene: HGFAC
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - HEPATOCYTE GROWTH FACTOR ACTIVATOR
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: VIRUS
    Gene: HGFAC
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:74 , NAG A:742 , HOH A:809 , ASP L:151 , ASN L:152 , HIS L:189BINDING SITE FOR RESIDUE NAG A 741
2AC2SOFTWAREGLY A:36 , ASP A:39 , NAG A:741 , BMA A:743BINDING SITE FOR RESIDUE NAG A 742
3AC3SOFTWARENAG A:742BINDING SITE FOR RESIDUE BMA A 743

(-) SS Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:58
2A:50 -A:111D
3A:122 -B:393
4A:136 -A:201
5A:168 -A:182
6A:191 -A:220
7H:22 -H:92
8H:140 -H:196
9L:23 -L:88
10L:134 -L:194
11L:214 -H:216

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Thr L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:146 -Pro H:147
5Glu H:148 -Pro H:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024295R644QHGFA_HUMANPolymorphism2498323AR241Q
2UniProtVAR_024294R509HHGFA_HUMANPolymorphism16844401AR111CH
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.HGFA_HUMAN408-646  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.HGFA_HUMAN443-448  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.HGFA_HUMAN592-603  1A:189-200

(-) Exons   (5, 6)

Asymmetric/Biological Unit (5, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003827741aENSE00001493344chr4:3443614-3443845232HGFA_HUMAN1-39390--
1.2ENST000003827742ENSE00000699356chr4:3444459-3444639181HGFA_HUMAN40-100610--
1.3ENST000003827743ENSE00000699357chr4:3444777-344487397HGFA_HUMAN100-132330--
1.4ENST000003827744ENSE00000699358chr4:3445068-344514780HGFA_HUMAN132-159280--
1.5ENST000003827745ENSE00000699359chr4:3445766-3445888123HGFA_HUMAN159-200420--
1.6aENST000003827746aENSE00000699360chr4:3446038-3446169132HGFA_HUMAN200-244450--
1.7ENST000003827747ENSE00001267259chr4:3446350-3446460111HGFA_HUMAN244-281380--
1.8ENST000003827748ENSE00001267254chr4:3446546-3446720175HGFA_HUMAN281-339590--
1.9aENST000003827749aENSE00000699364chr4:3446992-344707786HGFA_HUMAN339-368300--
1.10bENST0000038277410bENSE00000699365chr4:3447769-3448021253HGFA_HUMAN368-452852A:16-60B (gaps)
B:388-397		47
10
1.11ENST0000038277411ENSE00000699367chr4:3449219-3449358140HGFA_HUMAN452-499481A:60B-104
-		48
-
1.12ENST0000038277412ENSE00000699371chr4:3449622-3449762141HGFA_HUMAN499-546481A:104-147
-		48
-
1.13bENST0000038277413bENSE00000699372chr4:3449855-3450003149HGFA_HUMAN546-595501A:147-192
-		50
-
1.14cENST0000038277414cENSE00001493333chr4:3450964-3451211248HGFA_HUMAN596-655601A:193-243 (gaps)
-		52
-

(-) Sequences/Alignments

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 2r0lA01     2r0lA02 A:28-120,A:231-243 Trypsin-like serine proteases                                            2r0lA01 A:16-27,A:121-230 Trypsin-like serine proteases                                                           2r0lA02       CATH domains
               Pfam domains Trypsin-2r0lA01 A:16-238                                                                                                                                                                                                                  ----- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeee..eeeehhhhhh...hhh.eeeee............eee.eeeeee..............eeeee..............................eeeeee...............eeeeee..hhhhhh....hhhhh...eeee................eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhhh 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)
                2r0l 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 B from PDB  Type:PROTEIN  Length:10
 aligned with HGFA_HUMAN | Q04756 from UniProtKB/Swiss-Prot  Length:655

    Alignment length:10
                                   398
          HGFA_HUMAN    389 PGRQACGRRH  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) Exon 1.10b Transcript 1 (1)
           Transcript 1 (2) ---------- Transcript 1 (2)
                2r0l B  388 PGRQACGRRH  397
                                   397


Chain H from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               SCOP domains d2r0lh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                       d2r0lh2 H:114-212 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                    ---- SCOP domains
               CATH domains 2r0lH01 H:1-113 Immunoglobulins                                                                                      2r0lH02 H:114-216 Immunoglobulins                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhhheeeeee.....eeeeeeeehhhheeee.......eeeeee....eeeeee...hhhhheeeeeeee....eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2r0l H    1 EVQLVESGGGLVQPGGSLRLSCAASGFTISNSGIHWVRQAPGKGLEWVGWIYPTGGATDYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFWWRSFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126       136       146       156       166       176       186       196       206       216
                                                                              52A                            82A||                                                                                                                                      
                                                                                                              82B|                                                                                                                                      
                                                                                                               82C                                                                                                                                      


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2r0lL01 L:1-108 Immunoglobulins                                                                             2r0lL02 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..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2r0l 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)
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_PA (797)

(-) Gene Ontology  (7, 7)

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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

(-) Related Entries Specified in the PDB File

1ybw HGFA PROTEASE DOMAIN WITH NO INHIBITOR
1yc0 HGFA PROTEASE DOMAIN WITH KUNITZ DOMAIN FROM HAI-1
2r0k HGFA PROTEASE DOMAIN WITH INHIBITORY FAB58