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(-) Description

Title :  STRUCTURE OF HUMAN ACTIVATED THROMBIN-ACTIVATABLE FIBRINOLYSIS INHIBITOR, TAFIA, IN COMPLEX WITH TICK-DERIVED FUNNELIN INHIBITOR, TCI.
 
Authors :  L. Sanglas, J. L. Arolas, Z. Valnickova, F. X. Aviles, J. J. Enghild, F. X Ruth
Date :  01 Feb 10  (Deposition) - 16 Feb 10  (Release) - 02 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fibrinolysis, Cogaulation, Funnelin, Alpha-Beta-Hydrolase, Metallopeptidase, Alternative Splicing, Carboxypeptidase, Disulfide Bond, Glycoprotein, Hydrolase, Metal-Binding, Metalloprotease, Polymorphism, Protease, Secreted, Zinc, Zymogen, Blood Coagulation, Metalloenzyme Inhibitor, Metalloprotease Inhibitor, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Sanglas, J. L. Arolas, Z. Valnickova, F. X. Aviles, J. J. Enghild, F. X. Gomis-Ruth
Insights Into The Molecular Inactivation Mechanism Of Human Activated Thrombin-Activatable Fibrinolysis Inhibitor
J. Thromb. Haemost. V. 8 1056 2010
PubMed-ID: 20088943  |  Reference-DOI: 10.1111/J.1538-7836.2010.03740.X

(-) Compounds

Molecule 1 - CARBOXYPEPTIDASE B2
    ChainsA
    EC Number3.4.17.20
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTAFI, CARBOXYPEPTIDASE U, CPU, THROMBIN-ACTIVABLE FIBRINOLYSIS INHIBITOR, PLASMA CARBOXYPEPTIDASE B, PCPB
    TissueBLOOD SERUM
 
Molecule 2 - CARBOXYPEPTIDASE INHIBITOR
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPBAT-4-OMPA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificRHIPICEPHALUS BURSA
    Organism Taxid67831
    SynonymTICK-DERIVED FUNNELIN INHIBITOR, TCI

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 12)

Asymmetric/Biological Unit (6, 12)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL3Ligand/IonCHLORIDE ION
3GLY1Mod. Amino AcidGLYCINE
4GOL4Ligand/IonGLYCEROL
5K2Ligand/IonPOTASSIUM ION
6ZN1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:69 , GLU A:72 , HIS A:196 , LEU B:74BINDING SITE FOR RESIDUE ZN A 309
02AC2SOFTWAREHIS A:69 , ARG A:127 , ASN A:144 , ARG A:145 , TYR A:248 , LEU B:74BINDING SITE FOR RESIDUE GLY A 501
03AC3SOFTWAREGLY B:39 , CYS B:40 , LYS B:41 , SER B:63BINDING SITE FOR RESIDUE GOL B 502
04AC4SOFTWAREPHE A:132 , ILE A:139 , CYS A:166 , GLY A:167 , HOH A:526 , HOH A:528 , HOH A:530BINDING SITE FOR RESIDUE GOL A 503
05AC5SOFTWARESER A:5 , GLY A:84 , HIS A:85 , GLN A:88BINDING SITE FOR RESIDUE GOL A 504
06AC6SOFTWARETRP A:73 , ARG A:124 , PHE A:279 , LEU A:280 , LEU A:281 , GLY B:7 , PHE B:8BINDING SITE FOR RESIDUE GOL A 505
07AC7SOFTWARETYR A:118BINDING SITE FOR RESIDUE CL A 506
08AC8SOFTWAREHIS A:137 , SER A:160 , CA A:509BINDING SITE FOR RESIDUE CL A 507
09AC9SOFTWARECA A:509 , SER B:28BINDING SITE FOR RESIDUE CL B 508
10BC1SOFTWARELYS A:122 , SER A:159 , CYS A:161 , CL A:507 , CL B:508BINDING SITE FOR RESIDUE CA A 509
11BC2SOFTWAREGLN A:95 , ARG A:306BINDING SITE FOR RESIDUE K A 510
12BC3SOFTWAREASN A:16 , GLY B:67BINDING SITE FOR RESIDUE K A 511

(-) SS Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1A:66 -A:79
2A:138 -A:161
3A:152 -A:166
4B:3 -B:31
5B:10 -B:27
6B:16 -B:32
7B:40 -B:70
8B:47 -B:64
9B:54 -B:71

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:197 -Tyr A:198
2Pro A:205 -Tyr A:206
3Arg A:272 -Asp A:273

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_032565A169TCBPB2_HUMANPolymorphism3742264AA57T
2UniProtVAR_022258I347TCBPB2_HUMANPolymorphism1926447AT233T

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LMS)

(-) Exons   (0, 0)

(no "Exon" information available for 3LMS)

(-) 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:309
 aligned with CBPB2_HUMAN | Q96IY4 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:309
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414         
         CBPB2_HUMAN    115 ASASYYEQYHSLNEIYSWIEFITERHPDMLTKIHIGSSFEKYPLYVLKVSGKEQAAKNAIWIDCGIHAREWISPAFCLWFIGHITQFYGIIGQYTNLLRLVDFYVMPVVNVDGYDYSWKKNRMWRKNRSFYANNHCIGTDLNRNFASKHWCEEGASSSSCSETYCGLYPESEPEVKAVASFLRRNINQIKAYISMHSYSQHIVFPYSYTRSKSKDHEELSLVASEAVRAIEKISKNTRYTHGHGSETLYLAPGGGDDWIYDLGIKYSFTIELRDTGTYGFLLPERYIKPTCREAFAAVSKIAWHVIRNV  423
               SCOP domains d3lmsa_ A: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------Peptidase_M14-3lmsA01 A:18-296                                                                                                                                                                                                                                                             ------------ Pfam domains
         Sec.struct. author ..hhhhhh..hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee........eeeeeee......hhhhhhhhhhhhhhhhh...hhhhhhhhhheeeeee...hhhhhhhhhhh...................hhhhh...........................hhhhhhhhhhhhhh...eeeeeeee....eeee..........hhhhhhhhhhhhhhhhhhhh.....eeeehhhhh.....hhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------T---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3lms A    4 ASASYYEQYHSLNEIYSWIEFITERHPDMLTKIHIGSSFEKYPLYVLKVSGKEQAAKNAIWIDCGIHAREWISPAFCLWFIGHITQFYGIIGQYTNLLRLVDFYVMPVVNVDGYDYSWKKNRMWRKNRSFYANNHCIGTDLNRNFASKHWCEEGASSSSCSETYCGLYPESEPEVKAVASFLRRNINQIKAYISMHSYSQHIVFPYSYTRSKSKDHEELSLVASEAVRAIEKTSKNTRYTHGHGSETLYLAPGGGDDWIYDLGIKYSFTIELRDTGTYGFLLPERYIKPTCREAFAAVSKIAWHVIRNV  308
                                    13        23        33        43        53  |||   62        72        82        92       102       112       122       132       142       151       161       171       181      |190       200       210       220       230    |||239       249       259       269       279       289       299         
                                                                               56||                                                                                          150||                                  188||                                           235||                                                                        
                                                                               567|                                                                                          1501|                                  1889|                                           2356|                                                                        
                                                                                 57                                                                                            151                                    189                                             236                                                                        

Chain B from PDB  Type:PROTEIN  Length:74
 aligned with TCI1_RHIBU | Q5EPH2 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:74
                                    32        42        52        62        72        82        92    
          TCI1_RHIBU     23 NECVSKGFGCLPQSDCPQEARLSYGGCSTVCCDLSKLTGCKGKGGECNPLDRQCKELQAESASCGKGQKCCVWL   96
               SCOP domains d3lmsb1 B:1-37                       d3lmsb2 B:38-74                       SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains Inhibitor_I68-3lmsB01 B:1-74                                               Pfam domains
         Sec.struct. author hhhhhh..eeehhhhhhhh.ee.......eee.hhhh..hhhhh.eeee.....ee.hhhhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                3lms B    1 NECVSKGFGCLPQSDCPQEARLSYGGCSTVCCDLSKLTGCKGKGGECNPLDRQCKELQAESASCGKGQKCCVWL   74
                                    10        20        30        40        50        60        70    

   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, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (30, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CBPB2_HUMAN | Q96IY4)
molecular function
    GO:0004180    carboxypeptidase activity    Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
    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:0004181    metallocarboxypeptidase activity    Catalysis of the hydrolysis of C-terminal amino acid residues from a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0071333    cellular response to glucose stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
    GO:0042730    fibrinolysis    A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0097421    liver regeneration    The regrowth of lost or destroyed liver.
    GO:0051918    negative regulation of fibrinolysis    Any process that stops, prevents, or reduces the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.
    GO:2000346    negative regulation of hepatocyte proliferation    Any process that stops, prevents or reduces the frequency, rate or extent of hepatocyte proliferation.
    GO:0010757    negative regulation of plasminogen activation    Any process that decreases the rate, frequency or extent of plasminogen activation. Plasminogen activation is the process in which plasminogen is processed to plasmin.
    GO:0003331    positive regulation of extracellular matrix constituent secretion    Any process that increases the rate, frequency, or extent of the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0009408    response to heat    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
    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.
    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.

Chain B   (TCI1_RHIBU | Q5EPH2)
molecular function
    GO:0004857    enzyme inhibitor activity    Binds to and stops, prevents or reduces the activity of an enzyme.
    GO:0008191    metalloendopeptidase inhibitor activity    Stops, prevents or reduces the activity of metalloendopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain and contain a chelated metal ion at their active sites which is essential to their catalytic activity.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
biological process
    GO:0044002    acquisition of nutrients from host    The process that begins with the production and formation of structures and molecules in an organism that are required for the acquisition and utilization of nutrients from its host organism, and the ends with the acquirement of the nutrients. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0042730    fibrinolysis    A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    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:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    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
        CBPB2_HUMAN | Q96IY43d66 3d67 3d68 4p10 5hvf 5hvg 5hvh
        TCI1_RHIBU | Q5EPH21zlh 1zli 2jto 2k2x 2k2y 2k2z 3d4u 3osl

(-) Related Entries Specified in the PDB File

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3d66 HUMAN TAFIA PRECURSOR, TAFI.
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