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(-) Description

Title :  COMPLEX OF BENZAMIDINE WITH THE CATALYTIC DOMAIN OF HUMAN TWO CHAIN TISSUE PLASMINOGEN ACTIVATOR [(TC)-T-PA]
 
Authors :  W. Bode, D. Lamba
Date :  10 Nov 95  (Deposition) - 11 Jan 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Serine Protease, Fibrinolytic Enzymes (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Lamba, M. Bauer, R. Huber, S. Fischer, R. Rudolph, U. Kohnert, W. Bode
The 2. 3 A Crystal Structure Of The Catalytic Domain Of Recombinant Two-Chain Human Tissue-Type Plasminogen Activator
J. Mol. Biol. V. 258 117 1996
PubMed-ID: 8613982  |  Reference-DOI: 10.1006/JMBI.1996.0238
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TWO CHAIN TISSUE PLASMINOGEN ACTIVATOR
    ChainsA
    EC Number3.4.21.68
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCATALYTIC DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym(TC)-T-PA
 
Molecule 2 - TWO CHAIN TISSUE PLASMINOGEN ACTIVATOR
    ChainsB
    EC Number3.4.21.68
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCATALYTIC DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym(TC)-T-PA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:42 , HIS B:57 , GLN B:192 , GLY B:193 , SER B:195 , ARG B:243 , BEN B:245 , HOH B:297BINDING SITE FOR RESIDUE PO4 B 1
2AC2SOFTWAREPO4 B:1 , ASP B:189 , ALA B:190 , GLN B:192 , SER B:195 , TRP B:215 , GLY B:219 , GLY B:226 , HOH B:261BINDING SITE FOR RESIDUE BEN B 245

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:1 -B:122
2B:42 -B:58
3B:50 -B:111
4B:136 -B:201
5B:168 -B:182
6B:191 -B:220

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RTF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RTF)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.TPA_HUMAN311-561  1B:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.TPA_HUMAN353-358  1B:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.TPA_HUMAN507-518  1B:189-200

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002208091aENSE00002112956chr8:42065242-42065012231TPA_HUMAN-00--
1.5ENST000002208095ENSE00002181240chr8:42050729-4205063298TPA_HUMAN1-24240--
1.6ENST000002208096ENSE00001617965chr8:42048932-4204889043TPA_HUMAN25-39150--
1.7bENST000002208097bENSE00001727998chr8:42046589-42046452138TPA_HUMAN39-85470--
1.8bENST000002208098bENSE00000692406chr8:42045534-42045424111TPA_HUMAN85-122380--
1.9dENST000002208099dENSE00001128022chr8:42045090-42044916175TPA_HUMAN122-180590--
1.9fENST000002208099fENSE00000692402chr8:42042690-4204259992TPA_HUMAN180-211320--
1.10aENST0000022080910aENSE00000692400chr8:42040408-42040237172TPA_HUMAN211-268580--
1.11ENST0000022080911ENSE00002184621chr8:42039540-4203945586TPA_HUMAN268-297300--
1.12bENST0000022080912bENSE00001674536chr8:42038203-42038008196TPA_HUMAN297-362661B:16-60B (gaps)52
1.13bENST0000022080913bENSE00001605389chr8:42037896-42037760137TPA_HUMAN362-408471B:60B-10447
1.14aENST0000022080914aENSE00001793485chr8:42037584-42037444141TPA_HUMAN408-455481B:104-14748
1.15ENST0000022080915ENSE00001758697chr8:42036581-42036415167TPA_HUMAN455-510561B:147-192 (gaps)56
1.16eENST0000022080916eENSE00002116161chr8:42033669-42032751919TPA_HUMAN511-562521B:193-244 (gaps)53

(-) 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:8
                                         
               SCOP domains d1rtf.1  SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                1rtf A   1A TCGLRQYS    7
                            |       
                           1A       

Chain B from PDB  Type:PROTEIN  Length:244
 aligned with TPA_HUMAN | P00750 from UniProtKB/Swiss-Prot  Length:562

    Alignment length:252
                                   320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560  
           TPA_HUMAN    311 IKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP  562
               SCOP domains d1rtf.1 A:,B: Two-chain    tissue plasminogen activator (TC)-T-PA                                                                                                                                                                                            SCOP domains
               CATH domains 1rtfB01     1rtfB02 B:2   8-120,B:233-242 Trypsin-like serine proteases                                               1rtfB01 B:16-27,B:121-232 Trypsin-like serine proteases                                                                   1rtfB02   -- CATH domains
               Pfam domains Trypsin-1rtfB01 B:16-23   8                                                                                                                                                                                                                           ------ Pfam domains
         Sec.struct. author ........hhh...eeeeee...---..eeeeeeeeee..eeee.hhhh.....hhheeeee............eeeeeeeeee.............eeeee..............................eeeeee...............eeeeee...hhh..............eeee.....-----............eeeeee..eeeeeeeeee..........eeeeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-243 UniProt: 311-561                                                                                                                                                                                                                - PROSITE (1)
                PROSITE (2) ------------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.12b  PDB: B:16-60B (gaps) UniProt: 297-362   ---------------------------------------------Exon 1.14a  PDB: B:104-147 UniProt: 408-455     -------------------------------------------------------Exon 1.16e  PDB: B:193-244 (gaps) UniProt: 511-562   Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.13b  PDB: B:60B-104 UniProt: 362-408    ----------------------------------------------Exon 1.15  PDB: B:147-192 (gaps) UniProt: 455-510       ---------------------------------------------------- Transcript 1 (2)
                1rtf B   16 IKGGLFADIASHPWQAAIFAKHR---GERFLCGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRS-----NLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP  244
                                    25        35  |   | 40        50        60||||    66        76        86        96       106    |||112       122       132       142       152       162       170       180      || -   |   192       202       212    || 222       232       242  
                                                37A 37E                     60A|||                                               110A|||                                                        169A|              186A|  186H                            217|  |                       
                                                                             60B||                                                110B||                                                         169B               186B                                   219  |                       
                                                                              60C|                                                 110C|                                                                                                                     221A                       
                                                                               60D                                                  110D                                                                                                                                                

   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B   (TPA_HUMAN | P00750)
molecular function
    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: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:0051219    phosphoprotein binding    Interacting selectively and non-covalently with a phosphorylated protein.
    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:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    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: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:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0042730    fibrinolysis    A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
    GO:0045861    negative regulation of proteolysis    Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
    GO:0031639    plasminogen activation    The process in which inactive plasminogen is processed to active plasmin. This process includes cleavage at an internal Arg-Val site to form an N-terminal A-chain and C-terminal B-chain held together by a disulfide bond, and can include further proteolytic cleavage events to remove the preactivation peptide.
    GO:0048008    platelet-derived growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of a platelet-derived growth factor receptor binding to one of its physiological ligands.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0001666    response to hypoxia    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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0014909    smooth muscle cell migration    The orderly movement of a smooth muscle cell from one site to another, often during the development of a multicellular organism.
cellular component
    GO:0045177    apical part of cell    The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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.
    GO:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TPA_HUMAN | P007501a5h 1bda 1pk2 1pml 1tpg 1tpk 1tpm 1tpn 5brr

(-) Related Entries Specified in the PDB File

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