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(-) Description

Title :  CRYSTAL STRUCTURE OF THROMBIN-ACTIVATABLE FIBRINOLYSIS INHIBITOR IN COMPLEX WITH AN INHIBITORY NANOBODY (VHH-A204)
 
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 :  3.05
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
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, C
    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, D
    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

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric Unit (5, 15)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2BMA1Ligand/IonBETA-D-MANNOSE
3MAN2Ligand/IonALPHA-D-MANNOSE
4NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
5ZN2Ligand/IonZINC ION
Biological Unit 1 (4, 9)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2BMA1Ligand/IonBETA-D-MANNOSE
3MAN2Ligand/IonALPHA-D-MANNOSE
4NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2BMA-1Ligand/IonBETA-D-MANNOSE
3MAN-1Ligand/IonALPHA-D-MANNOSE
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
5ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:159 , GLU A:162 , HIS A:288 , ACT A:510binding site for residue ZN A 509
02AC2SOFTWAREGLU A:162 , ARG A:217 , SER A:289 , GLU A:363 , ZN A:509binding site for residue ACT A 510
03AC3SOFTWAREHIS C:159 , GLU C:162 , HIS C:288 , GLU C:363 , ACT C:505binding site for residue ZN C 504
04AC4SOFTWAREHIS C:159 , ARG C:217 , ASN C:234 , ARG C:235 , TYR C:341 , GLU C:363 , ZN C:504binding site for residue ACT C 505
05AC5SOFTWAREASN A:22 , THR A:26 , TYR A:27 , HIS A:61 , ASP C:120binding site for Poly-Saccharide residues NAG A 501 through MAN A 505 bound to ASN A 22
06AC6SOFTWAREGLU A:28 , ASN A:51 , ALA A:52 , SER A:53binding site for Mono-Saccharide NAG A 506 bound to ASN A 51
07AC7SOFTWAREASN A:63binding site for Mono-Saccharide NAG A 507 bound to ASN A 63
08AC8SOFTWAREASN A:86 , VAL A:89 , SER A:96 , GLN A:100 , GLU A:376binding site for Mono-Saccharide NAG A 508 bound to ASN A 86
09AC9SOFTWAREASN C:22binding site for Poly-Saccharide residues NAG C 501 through NAG C 502 bound to ASN C 22
10AD1SOFTWAREGLU C:28 , ASN C:51binding site for Mono-Saccharide NAG C 503 bound to ASN C 51

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:156 -A:169
2A:228 -A:252
3A:243 -A:257
4B:22 -B:95
5C:156 -C:169
6C:228 -C:252
7C:243 -C:257
8D:22 -D:95

(-) Cis Peptide Bonds  (8, 8)

Asymmetric 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
5Gln C:33 -Pro C:34
6Ser C:289 -Tyr C:290
7Pro C:297 -Tyr C:298
8Arg C:365 -Asp C:366

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HVG)

(-) Sequences/Alignments

Asymmetric 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..hhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh........hhhhhh..hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee........eeeeee.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhheeeeee...hhhhhhhhhhh...................hhhhh...........................hhhhhhhhhhhhhh...eeeeeeeee...eeee..........hhhhhhhhhhhhhhhhhhhh.....eeeehhhhh.....hhhhhhhh....eeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hvg 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:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..eee.....eeeeee.hhhhhh...eeeeee.....eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeee.hhhhh.hhhhh......eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hvg B   1 QVQLQESGGGLVQPGGSLRLSCAASGSIFSGNAMGWYRQAPGKQRELVAAITSGGSTDYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCHVDPRPWGYDVTDYDYWGQGTQVTVSS 122
                                    10        20        30        40        50        60        70        80        90       100       110       120  


Chain C from PDB  Type:PROTEIN  Length:400
                                                                                                                                                                                                                                                                                                                                                                                                                                                
               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...eeeeeeee.....eeeeeee........eeeeee.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhheeeeee...hhhhhhhhhhh...................hhhhh...........................hhhhhhhhhhhhhh...eeeeeeee....eeee..........hhhhhhhhhhhhhhhhhhhh.....eeeehhhhh.....hhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hvg C   2 QSGQVLAALPRTSRQVQVLQNLTTTYEIVLWQPVTADLIVKKKQVHFFVNASDVDNVKAHLNVSGIPCSVLLADVEDLIQQQISNDTVSPRASASYYEQYHSLNEIYSWIEFITERHPDMLTKIHIGSSFEKYPLYVLKVSGKEQAAKNAIWIDCGIHAREWISPAFCLWFIGHITQFYGIIGQYTNLLRLVDFYVMPVVNVDGYDYSWKKNRMWRKNRSFYANNHCIGTDLNRNFASKHWCEEGASSSSCSETYCGLYPESEPEVKAVASFLRRNINQIKAYISMHSYSQHIVFPYSYTRSKCKDHEELSLVASEAVRAIEKISKNIRYTYGQGSETLYLAPGGGDDWIYDLGIKYSFTIELRDTGTYGFLLPERYIKPTCREAFAAVSKIAWHVIRNV 401
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401


Chain D from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..ee......eeeeeeehhhhhh...eeeeee.....eeeeeee.....eee........eeeee....eeeeee...hhhhheeeeeee.hhhhh.hhhhh......eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 5hvg D   2 VQLQESGGGLVQPGGSLRLSCAASGSIFSGNAMGWYRQAPGKQRELVAAITSGGSTDYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCHVDPRPWGYDVTDYDYWGQGTQVTV 120
                                    11        21        31        41        51        61        71        81        91       101       111
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:365 - Asp A:366   [ RasMol ]  
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  5hvg
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 Related Entries

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

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        CBPB2_HUMAN | Q96IY4: 3d66 3d67 3d68 3lms 4p10 5hvf 5hvh

(-) Related Entries Specified in the PDB File

5hvf 5HVF CONTAINS THE SAME PROTEIN (TAFI) COMPLEXED WITH A DIFFERENT NANOBODY.
5hvh 5HVH IS A TRIPLE COMPLEX WHICH CONTAINS THE SAME PROTEIN (TAFI) COMPLEXED WITH THIS NANOBODY AND ANOTHER DIFFERENT NANOBODY.