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(-) Description

Title :  CRYSTAL STRUCTURE OF THROMBIN-ACTIVATABLE FIBRINOLYSIS INHIBITOR IN COMPLEX WITH TWO INHIBITORY NANOBODIES
 
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 :  3.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Procarboxypeptidase U, Thrombin-Activatable Fibrinolysis Inhibitor, Tafi, Procarboxypeptidase R, Plasma Procarboxypeptidase B, Nanobody, Antibody Fragment, Protein Complex, Hydrolase/Hydrolase Inhibitor, 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
    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-A204
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHEN6
    Expression System Strain: WK6
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: ALPACA
    Organism Scientific: VICUGNA PACOS
    Organism Taxid: 30538
    Synonym: NANOBODY
 
Molecule 3 - VHH-I83
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHEN6
    Expression System Strain: WK6
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: ALPACA
    Organism Scientific: VICUGNA PACOS
    Organism Taxid: 30538
    Synonym: NANOBODY

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
2ZN1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:159 , GLU A:162 , HIS A:288binding site for residue ZN A 508
2AC2SOFTWAREASN A:22 , THR A:25binding site for Poly-Saccharide residues NAG A 501 through NAG A 502 bound to ASN A 22
3AC3SOFTWARESER A:3 , GLU A:28 , ASN A:51 , ALA A:52 , SER A:53binding site for Poly-Saccharide residues NAG A 503 through NAG A 504 bound to ASN A 51
4AC4SOFTWAREASN A:63 , VAL C:54 , GLY C:55 , SER C:56 , THR C:57binding site for Poly-Saccharide residues NAG A 505 through NAG A 506 bound to ASN A 63
5AC5SOFTWAREASN A:86 , GLN A:100 , GLU A:376binding site for Mono-Saccharide NAG A 507 bound to ASN A 86

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:156 -A:169
2A:228 -A:252
3A:243 -A:257
4B:22 -B:95
5C:22 -C:94

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HVH)

(-) 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:401
                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhh.eeeee..hhhhh.....eeeeee..hhhhhhhhhhhh...eeeee.hhhhhhhhhhhh.......hhhhhhh..hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee........eeeeee.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhheeeeee...hhhhhhhhhhh...................hhhhh...........................hhhhhhhhhhhhhh...eeeeeeeee...eee.hhhhhh......hhhhhhhhhhhhhhhhhh.....ee............hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hvh A   1 FQSGQVLAALPRTSRQVQVLQNLTTTYEIVLWQPVTADLIVKKKQVHFFVNASDVDNVKAHLNVSGIPCSVLLADVEDLIQQQISNDTVSPRASASYYEQYHSLNEIYSWIEFITERHPDMLTKIHIGSSFEKYPLYVLKVSGKEQAAKNAIWIDCGIHAREWISPAFCLWFIGHITQFYGIIGQYTNLLRLVDFYVMPVVNVDGYDYSWKKNRMWRKNRSFYANNHCIGTDLNRNFASKHWCEEGASSSSCSETYCGLYPESEPEVKAVASFLRRNINQIKAYISMHSYSQHIVFPYSYTRSKCKDHEELSLVASEAVRAIEKISKNIRYTYGQGSETLYLAPGGGDDWIYDLGIKYSFTIELRDTGTYGFLLPERYIKPTCREAFAAVSKIAWHVIRNV 401
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400 


Chain B from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eee.....eeeeeeehhhhhh...eeeeee.....eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeee.hhhhh.hhhhh......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hvh B   3 QLQESGGGLVQPGGSLRLSCAASGSIFSGNAMGWYRQAPGKQRELVAAITSGGSTDYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCHVDPRPWGYDVTDYDYWGQGTQVTVSS 122
                                    12        22        32        42        52        62        72        82        92       102       112       122


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

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 ]  
    Ser A:289 - Tyr A:290   [ RasMol ]  
 

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

5hvf 5HVF IS A BINARY COMPLEX CONTAINING THE SAME TWO PROTEINS (TAFI, VHH-I83) AS IN THIS TRIPLE COMPLEX STRUCTURE.
5hvg 5HVG IS A BINARY COMPLEX CONTAINING THE SAME TWO PROTEINS (TAFI, VHH-A204) AS IN THIS TRIPLE COMPLEX STRUCTURE.