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(-) Description

Title :  CRYSTAL STRUCTURE OF THROMBIN-ACTIVATABLE FIBRINOLYSIS INHIBITOR IN COMPLEX WITH AN INHIBITORY NANOBODY (VHH-I83)
 
Authors :  X. Zhou, S. D. Weeks, S. V. Strelkov, P. J. Declerck
Date :  28 Jan 16  (Deposition) - 22 Jun 16  (Release) - 31 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Procarboxypeptidase U, Thrombin-Activatable Fibrinolysis Inhibitor, Tafi, Procarboxypeptidase R, Plasma Procarboxypeptidase B, Nanobody, Antibody Fragment, Protein Complex, Hydrolase/Hydrolase Inhibitor, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zhou, S. D. Weeks, P. Ameloot, N. Callewaert, S. V. Strelkov, P. J. Declerck
Elucidation Of The Molecular Mechanisms Of Two Nanobodies That Inhibit Thrombin-Activatable Fibrinolysis Inhibitor Activation And Activated Thrombin-Activatable Fibrinolysis Inhibitor Activity.
J. Thromb. Haemost. V. 14 1629 2016
PubMed-ID: 27279497  |  Reference-DOI: 10.1111/JTH.13381

(-) Compounds

Molecule 1 - CARBOXYPEPTIDASE B2
    Chains: A
    EC Number: 3.4.17.20
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPIC9
    Expression System Strain: M5
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 23-423
    Gene: CPB2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CARBOXYPEPTIDASE U,CPU,PLASMA CARBOXYPEPTIDASE B,PCPB, THROMBIN-ACTIVABLE FIBRINOLYSIS INHIBITOR,TAFI
 
Molecule 2 - VHH-I83
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETHSUK
    Expression System Strain: ROSETTA2 PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: ALPACA
    Organism Scientific: VICUGNA PACOS
    Organism Taxid: 30538

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2FLC1Ligand/IonCITRATE ANION
3MAN1Ligand/IonALPHA-D-MANNOSE
4NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
5ZN1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:159 , GLU A:162 , HIS A:288 , FLC A:509binding site for residue ZN A 508
2AC2SOFTWAREHIS A:159 , GLU A:162 , ARG A:217 , ASN A:234 , ARG A:235 , SER A:299 , LEU A:340 , TYR A:341 , ALA A:343 , GLU A:363 , ZN A:508binding site for residue FLC A 509
3AC3SOFTWAREARG A:15 , ASN A:22 , THR A:26 , HIS A:61 , HOH A:606 , HOH A:614 , GLN B:39 , VAL B:91 , TYR B:93 , GLN B:111 , GLY B:112binding site for Poly-Saccharide residues NAG A 501 through MAN A 504 bound to ASN A 22
4AC4SOFTWAREGLU A:28 , ASN A:51 , SER A:53binding site for Mono-Saccharide NAG A 505 bound to ASN A 51
5AC5SOFTWAREASN A:63 , HOH A:608 , VAL B:54 , GLY B:55 , SER B:56 , THR B:57binding site for Mono-Saccharide NAG A 506 bound to ASN A 63
6AC6SOFTWAREGLN A:82 , ASN A:86 , VAL A:89 , GLN A:100 , GLU A:376binding site for Mono-Saccharide NAG A 507 bound to ASN A 86

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:156 -A:169
2A:228 -A:252
3A:243 -A:257
4B:22 -B:94

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gln A:33 -Pro A:34
2Ser A:289 -Tyr A:290
3Pro A:297 -Tyr A:298
4Arg A:365 -Asp A:366

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HVF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HVF)

(-) Exons   (0, 0)

(no "Exon" information available for 5HVF)

(-) 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:372
                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhh.eeeee..hhhhh.....eeeeee..hhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh........hhhhhh..hhhhhhhhhhhhhhhh....eeeeeee.....eeeeee..eeee.......hhhhhhhhhhhhhh.eeee...hhhhhhhhhhh...................hhhhh...........................hhhhhhhhhhhhhh.....eeeeeee...eeee..........hhhhhhhhhhhhhhhhhhhh.....eeeehhhhh.....hhhhhhhh....eeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hvf A   2 QSGQVLAALPRTSRQVQVLQNLTTTYEIVLWQPVTADLIVKKKQVHFFVNASDVDNVKAHLNVSGIPCSVLLADVEDLIQQQISNDTVSPRASASYYEQYHSLNEIYSWIEFITERHPDMLTKIHIGSSFEKYPLYVLKVAIWIDCGIHAREWISPAFCLWFIGHIDFYVMPVVNVDGYDYSWKKNRMWRKNRSFYANNHCIGTDLNRNFASKHWCEEGASSSSCSETYCGLYPESEPEVKAVASFLRRNINQIKAYISMHSYSQHIVFPYSYTRSKCKDHEELSLVASEAVRAIEKISKNIRYTYGQGSETLYLAPGGGDDWIYDLGIKYSFTIELRDTGTYGFLLPERYIKPTCREAFAAVSKIAWHVIR 399
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141|      160       170     ||197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397  
                                                                                                                                                                     141|                      176|                                                                                                                                                                                                             
                                                                                                                                                                      151                       194                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:118
                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eee.....eeeeeeee.......eeeeeee......eeeeee....eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeeeee...eeeeee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 5hvf B   2 VQLQESGGGLVQAGGSLRLSCAASGSIFSPNAMGWYRQAPGKERELVAARTNVGSTYADSVKGRFTVSRDNAKNTVYLQMNSLKPEDTAVYYCNAWGQDGWLGQYDYWGQGTQVTVSS 119
                                    11        21        31        41        51        61        71        81        91       101       111
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 5HVF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HVF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HVF)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:365 - Asp A:366   [ RasMol ]  
    Gln A:33 - Pro A:34   [ RasMol ]  
    Pro A:297 - Tyr A:298   [ RasMol ]  
    Ser A:289 - Tyr A:290   [ RasMol ]  
 

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 Related Entries

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UniProtKB/Swiss-Prot
        CBPB2_HUMAN | Q96IY4: 3d66 3d67 3d68 3lms 4p10 5hvg 5hvh

(-) Related Entries Specified in the PDB File

5hvg 5hvh