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(-) Description

Title :  CATALYTIC FRAGMENT OF MASP-2 IN COMPLEX WITH ITS SPECIFIC INHIBITOR DEVELOPED BY DIRECTED EVOLUTION ON SGCI SCAFFOLD
 
Authors :  D. Heja, V. Harmat, J. Dobo, R. Szasz, K. A. Kekesi, P. Zavodszky, P. Gal,
Date :  20 Sep 11  (Deposition) - 25 Apr 12  (Release) - 27 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.28
Chains :  Asym./Biol. Unit :  A,B,I
Keywords :  In Vitro Evolution, Specific Inhibitor, Allostery, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Heja, V. Harmat, K. Fodor, M. Wilmanns, J. Dobo, K. A. Kekesi, P. Zavodszky, P. Gal, G. Pal
Monospecific Inhibitors Show That Both Mannan-Binding Lectin-Associated Serine Protease-1 (Masp-1) And -2 Are Essential For Lectin Pathway Activation And Reveal Structural Plasticity Of Masp-2.
J. Biol. Chem. V. 287 20290 2012
PubMed-ID: 22511776  |  Reference-DOI: 10.1074/JBC.M112.354332

(-) Compounds

Molecule 1 - MANNAN-BINDING LECTIN SERINE PROTEASE 2 A CHAIN
    ChainsA
    EC Number3.4.21.104
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-17B
    Expression System StrainBL21 DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentSUSHI 2 DOMAIN RESIDUES 363-444
    GeneMASP2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMANNAN-BINDING LECTIN SERINE PROTEASE 2, MBL-ASSOCIATED SERINE PROTEASE 2, MANNOSE-BINDING PROTEIN-ASSOCIATED SERINE PROTEASE 2, MASP-2
 
Molecule 2 - MANNAN-BINDING LECTIN SERINE PROTEASE 2 B CHAIN
    ChainsB
    EC Number3.4.21.104
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-17B
    Expression System StrainBL21 DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentPEPTIDASE S1 DOMAIN RESIDUES 445-686
    GeneMASP2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMANNAN-BINDING LECTIN SERINE PROTEASE 2, MBL-ASSOCIATED SERINE PROTEASE 2, MANNOSE-BINDING PROTEIN-ASSOCIATED SERINE PROTEASE 2, MASP-2
 
Molecule 3 - PROTEASE INHIBITOR SGPI-2
    ChainsI
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMAL-TEV-SGPI
    Expression System StrainBL21 STAR
    Expression System Taxid511693
    Expression System VectorPMAL-P2G
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonDESERT LOCUST
    Organism ScientificSCHISTOCERCA GREGARIA
    Organism Taxid7010
    SynonymSCHISTOCERCA GREGARIA CHYMOTRYPSIN INHIBITOR, SGCI

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABI

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:169 , HOH B:227 , HOH B:290 , ARG B:578 , ARG B:583 , ASN B:584 , MET B:586BINDING SITE FOR RESIDUE SO4 B 1

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:366 -A:412
2A:396 -A:430
3A:434 -B:552
4B:598 -B:618
5B:629 -B:660
6I:4 -I:19
7I:14 -I:33
8I:17 -I:28

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro B:605 -Pro B:606

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_028785D371YMASP2_HUMANPolymorphism12711521AD371Y
2UniProtVAR_028786V377AMASP2_HUMANPolymorphism2273346AV377A
3UniProtVAR_075088V405MMASP2_HUMANPolymorphism61735594AV405M
4UniProtVAR_028787R439HMASP2_HUMANPolymorphism12085877AR439H

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

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PACIFASTINPS51446 Pacifastin domain profile.SGP1_SCHGR20-54
57-92
  1-
I:1-35
2SUSHIPS50923 Sushi/CCP/SCR domain profile.MASP2_HUMAN298-363
364-432
  1-
A:364-432
3TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.MASP2_HUMAN445-684  1B:445-684
4TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.MASP2_HUMAN627-638  1B:627-638

(-) Exons   (4, 5)

Asymmetric/Biological Unit (4, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1dENST000004008971dENSE00001833377chr1:11107280-1110726021MASP2_HUMAN1-220--
1.2ENST000004008972ENSE00000818831chr1:11107176-11106948229MASP2_HUMAN2-78770--
1.3aENST000004008973aENSE00000472116chr1:11106790-11106613178MASP2_HUMAN79-138600--
1.3cENST000004008973cENSE00000743093chr1:11105596-11105465132MASP2_HUMAN138-182450--
1.4ENST000004008974ENSE00000472118chr1:11103592-11103396197MASP2_HUMAN182-247660--
1.5bENST000004008975bENSE00000743090chr1:11103079-11102932148MASP2_HUMAN248-297500--
1.6ENST000004008976ENSE00000472120chr1:11097868-11097750119MASP2_HUMAN297-336400--
1.7ENST000004008977ENSE00000743085chr1:11094963-1109488579MASP2_HUMAN337-363271A:362-363
-
2
-
1.8ENST000004008978ENSE00000743084chr1:11090939-11090805135MASP2_HUMAN363-408461A:363-408
-
46
-
1.9ENST000004008979ENSE00000472123chr1:11090307-1109023375MASP2_HUMAN408-433261A:408-433
-
26
-
1.10ENST0000040089710ENSE00000818830chr1:11087705-110865801126MASP2_HUMAN433-6862542A:433-444
B:445-686
12
242

(-) 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:83
 aligned with MASP2_HUMAN | O00187 from UniProtKB/Swiss-Prot  Length:686

    Alignment length:83
                                   371       381       391       401       411       421       431       441   
          MASP2_HUMAN   362 SIVDCGPPDDLPSGRVEYITGPGVTTYKAVIQYSCEETFYTMKVNDGKYVCEADGFWTSSKGEKSLPVCEPVCGLSARTTGGR 444
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee...........eeeeee....eee.....eeee.....eee.........eee............ Sec.struct. author
                 SAPs(SNPs) ---------Y-----A---------------------------M---------------------------------H----- SAPs(SNPs)
                PROSITE (1) SUSUSHI  PDB: A:364-432 UniProt: 364-432                               ------------ PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.---------------------------------------------------------------------Exon 1.10    Transcript 1 (1)
           Transcript 1 (2) -Exon 1.8  PDB: A:363-408 UniProt: 363-408     ------------------------------------ Transcript 1 (2)
           Transcript 1 (3) ----------------------------------------------Exon 1.9  PDB: A:408-433  ----------- Transcript 1 (3)
                 3tvj A 362 TIVDCGPPDDLPSGRVEYITGPGVTTYKAVIQYSCEETFYTMKVNDGKYVCDADGFWTSSKGEKSLPVCEPVCGLSARTTGGR 444
                                   371       381       391       401       411       421       431       441   

Chain B from PDB  Type:PROTEIN  Length:242
 aligned with MASP2_HUMAN | O00187 from UniProtKB/Swiss-Prot  Length:686

    Alignment length:242
                                   454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684  
          MASP2_HUMAN   445 IYGGQKAKPGDFPWQVLILGGTTAAGALLYDNWVLTAAHAVYEQKHDASALDIRMGTLKRLSPHYTQAWSEAVFIHEGYTHDAGFDNDIALIKLNNKVVINSNITPICLPRKEAESFMRTDDIGTASGWGLTQRGFLARNLMYVDIPIVDHQKCTAAYEKPPYPRGSVTANMLCAGLESGGKDSCRGDSGGALVFLDSETERWFVGGIVSWGSMNCGEAGQYGVYTKVINYIPWIENIISDF 686
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee..eeeeeee....eeeehhhhhh.........eeee..........eeeeeeeeee..............eeeee..................hhhhhh....eeeeee.............eeeeee..hhhhhhhhhhh...........eeee................eeeeee....eeeeeeeeeeee.........eeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:445-684 UniProt: 445-684                                                                                                                                                                                                    -- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.10  PDB: B:445-686 UniProt: 433-686 [INCOMPLETE]                                                                                                                                                                                            Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
           Transcript 1 (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 3tvj B 445 IYGGQKAKPGDFPWQVLILGGTTAAGALLYDNWVLTAAHAVYEQKHDASALDIRMGTLKRLSPHYTQAWSEAVFIHEGYTHDAGFDNDIALIKLNNKVVINSNITPICLPRKEAESFMRTDDIGTASGWGLTQRGFLARNLMYVDIPIVDHQKCTAAYEKPPYPRGSVTANMLCAGLESGGKDSCRGDSGGALVFLDSETERWFVGGIVSWGSMNCGEAGQYGVYTKVINYIPWIENIISDF 686
                                   454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684  

Chain I from PDB  Type:PROTEIN  Length:35
 aligned with SGP1_SCHGR | O46162 from UniProtKB/Swiss-Prot  Length:92

    Alignment length:35
                                    66        76        86     
           SGP1_SCHGR    57 EVTCEPGTTFKDKCNTCRCGSDGKSAACTLKACPQ  91
               SCOP domains d3tvji_ I: automated matches        SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author ........eeee..eeeee......eeee..ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE PACIFASTIN  PDB: I:1-35             PROSITE
                 Transcript ----------------------------------- Transcript
                 3tvj I   1 EVTCEPGTTFKDKCNTCRCGSDGKSAVCTKLWCNQ  35
                                    10        20        30     

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TVJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TVJ)

(-) Gene Ontology  (21, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MASP2_HUMAN | O00187)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0048306    calcium-dependent protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in the presence of calcium.
    GO:0001855    complement component C4b binding    Interacting selectively and non-covalently with the C4b product of the classical complement cascade.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0006956    complement activation    Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
    GO:0006958    complement activation, classical pathway    Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
    GO:0001867    complement activation, lectin pathway    Any process involved in the activation of any of the steps of the lectin pathway of the complement cascade which allows for the direct killing of microbes and the regulation of other immune processes.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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.

Chain I   (SGP1_SCHGR | O46162)
molecular function
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MASP2_HUMAN | O001871q3x 1szb 1zjk 4fxg 5jpm
        SGP1_SCHGR | O461621kgm 1kio 1kj0 2f91 2xtt 4djz

(-) Related Entries Specified in the PDB File

4djz