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(-) Description

Title :  CRYSTAL STRUCTURE OF HGFA IN COMPLEX WITH THE ALLOSTERIC INHIBITORY ANTIBODY FAB40
 
Authors :  R. Ganesan, C. Eigenbrot, S. Shia
Date :  30 Sep 09  (Deposition) - 15 Dec 09  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B,H,L
Keywords :  Serine Protease, Allosteric Inhibitor, Antibody, Egf-Like Domain, Glycoprotein, Fab Complex, Hydrolase, Disulfide Bond, Kringle, Protease, Secreted, Zymogen, Hydrolase-Immune System 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

(-) Compounds

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
    Synonym: HGF ACTIVATOR, HGFA
 
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
    Synonym: HGF ACTIVATOR, HGFA
 
Molecule 3 - ANTIBODY, FAB FRAGMENT, 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 - ANTIBODY, FAB FRAGMENT, 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

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:74 , HOH A:277 , HOH A:288 , HOH A:312 , NAG A:742 , ASP L:151 , ASN L:152 , HIS L:189BINDING SITE FOR RESIDUE NAG A 741
2AC2SOFTWAREASP A:39 , HOH A:300 , NAG A:741BINDING SITE FOR RESIDUE NAG A 742

(-) 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:219
7H:22 -H:92
8H:140 -H:196
9H:216 -L:214
10L:23 -L:88
11L:134 -L:194

(-) Cis Peptide Bonds  (5, 5)

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

 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:392-396		47
5
1.11ENST0000038277411ENSE00000699367chr4:3449219-3449358140HGFA_HUMAN452-499481A:60B-104
-		48
-
1.12ENST0000038277412ENSE00000699371chr4:3449622-3449762141HGFA_HUMAN499-546481A:104-145
-		46
-
1.13bENST0000038277413bENSE00000699372chr4:3449855-3450003149HGFA_HUMAN546-595501A:148-192
-		49
-
1.14cENST0000038277414cENSE00001493333chr4:3450964-3451211248HGFA_HUMAN596-655601A:193-243 (gaps)
-		51
-

(-) 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:233
 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 3k2uA01     3k2uA02 A:28-120,A:231-243 Trypsin-like serine proteases                                            3k2uA01 A:16-27,A:121-230   Trypsin-like serine proteases                                                         3k2uA02       CATH domains
               Pfam domains Trypsin-3k2uA01 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...hhhhhhhhh. 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:104-145 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:148-192 UniProt: 546-595       --------------------------------------------------- Transcript 1 (2)
                3k2u A   16 IIGGSSSLPGSHPWLAAIYIGDSFCAGSLVHTCWVVSAAHCFSHSPPRDSVSVVLGQHFFNRTTDVTQTFGIEKYIPYTLYSVFNPSDHDLVLIRLKKKGDRCATRSQFVQPICLPEPGSTFPAGHKCQIAGWGHLD--VSGYSSSLREALVPLVADHKCSSPEVYGADISPNMLCAGYFDCKSDACQGDSGGPLACEKNGVAYLYGIISW--GC--LHKPGVYTRVANYVDWINDRIR  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|||                               145  |                   170A|          184A 188A                         215  ||  |                     
                                                39                    60B||                                                  111B||                                  148                    170B                                               218|  |                     
                                                                       60C|                                                   111C|                                                                                                             219  |                     
                                                                        60D                                                    111D                                                                                                                222                     


Chain B from PDB  Type:PROTEIN  Length:5
 aligned with HGFA_HUMAN | Q04756 from UniProtKB/Swiss-Prot  Length:655

    Alignment length:5
          HGFA_HUMAN    393 ACGRR  397
               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)
                3k2u B  392 ACGRR  396


Chain H from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3k2uH01 H:1-113 Immunoglobulins                                                                                       3k2uH02 H:114-216 Immunoglobulins                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhheeeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.......ee...eeeee........eeeee....eeeeeeeeeee.....eeee.........ee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3k2u H    1 EVQLVESGGGLVQPGGSLRLSCAASGFTINGTYIHWVRQAPGKGLEWVGGIYPAGGATYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCAKWWAWPAFDYWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                                    10        20        30        40        50  |     59        69        79   |||  86        96   |   105       115       125 ||    141       151       161       171       181       191       201       211     
                                                                              52A                            82A||              100A                         127|                                                                                  
                                                                                                              82B|                                            134                                                                                  
                                                                                                               82C                                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                 
               SCOP domains d3k2ul1 L:1-107 automated matches                                                                          d3k2ul2 L:108-214 automated matches                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------3k2uL02 L:109-214 Immunoglobulins                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhh.eeeeeeee.......eeeeee........eeeee.......eeeeeeeehhhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3k2u L    1 DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSNRAPATFGQGTKVEIKRTVAAPSVFIFPPSDEQLTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120    || 133       143       153       163   ||  176       186       196       206        
                                                                                                                                                      125|                                   167|                                           
                                                                                                                                                       129                                    171
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

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

(-) CATH Domains  (2, 5)

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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  HGFA_HUMAN | Q04756
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 Related Entries

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

UniProtKB/Swiss-Prot
        HGFA_HUMAN | Q04756: 1ybw 1yc0 2r0k 2r0l 2wub 2wuc

(-) Related Entries Specified in the PDB File

1ybw 1yc0 2r0k 2r0l