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(-) Description

Title :  THE X-RAY STRUCTURE OF HUMAN ANGIOSTATIN
 
Authors :  M. C. Abad, R. K. Arni, D. K. Grella, F. J. Castellino, A. Tulinsky, J. H. Geiger
Date :  02 Dec 01  (Deposition) - 29 May 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Kringle Domains, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. C. Abad, R. K. Arni, D. K. Grella, F. J. Castellino, A. Tulinsky, J. H. Geiger
The X-Ray Crystallographic Structure Of The Angiogenesis Inhibitor Angiostatin.
J. Mol. Biol. V. 318 1009 2002
PubMed-ID: 12054798  |  Reference-DOI: 10.1016/S0022-2836(02)00211-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANGIOSTATIN
    ChainsA
    EC Number3.4.21.7
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System Taxid4922
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1BCN3Ligand/IonBICINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:115 , HIS A:198 , GLY A:199 , ILE A:201 , GLU A:221 , TRP A:225 , PHE A:227 , ARG A:234 , TRP A:235 , HOH A:548 , HOH A:571 , HOH A:636BINDING SITE FOR RESIDUE BCN A 335
2AC2SOFTWAREARG A:117 , ASP A:137 , ASP A:139 , TRP A:144 , ARG A:153 , TYR A:154 , THR A:287 , HOH A:711 , HOH A:725BINDING SITE FOR RESIDUE BCN A 336
3AC3SOFTWAREARG A:290 , LYS A:311 , TRP A:315 , HIS A:317 , ARG A:324 , TRP A:325 , HOH A:516 , HOH A:839BINDING SITE FOR RESIDUE BCN A 337

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:84 -A:162
2A:105 -A:145
3A:133 -A:157
4A:166 -A:243
5A:169 -A:297
6A:187 -A:226
7A:215 -A:238
8A:256 -A:333
9A:277 -A:316
10A:305 -A:328

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:112 -Pro A:113
2Ser A:194 -Pro A:195
3Thr A:284 -Pro A:285

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_016288H133QPLMN_HUMANPolymorphism4252186AH114Q
2UniProtVAR_033653R134KPLMN_HUMANPolymorphism2817AR115K
3UniProtVAR_018658L147PPLMN_HUMANDisease (PLGD)770198253AL128P
4UniProtVAR_018659R235HPLMN_HUMANDisease (PLGD)121918030AR216H
5UniProtVAR_016289R261HPLMN_HUMANPolymorphism4252187AR242H

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

(-) PROSITE Motifs  (2, 6)

Asymmetric/Biological Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KRINGLE_2PS50070 Kringle domain profile.PLMN_HUMAN102-181
184-262
274-352
376-454
480-560
  3A:83-162
A:165-243
A:255-333
-
-
2KRINGLE_1PS00021 Kringle domain signature.PLMN_HUMAN151-164
233-245
323-335
425-437
530-543
  3A:132-145
A:214-226
A:304-316
-
-

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003081921bENSE00001900502chr6:161123274-161123385112PLMN_HUMAN1-17170--
1.2dENST000003081922dENSE00002186994chr6:161127439-161127574136PLMN_HUMAN17-62460--
1.3aENST000003081923aENSE00002162767chr6:161128732-161128838107PLMN_HUMAN62-98370--
1.4aENST000003081924aENSE00002147931chr6:161132109-161132223115PLMN_HUMAN98-136391A:81-11737
1.5bENST000003081925bENSE00002160428chr6:161134018-161134157140PLMN_HUMAN136-183481A:117-16448
1.6ENST000003081926ENSE00002153394chr6:161135826-161135946121PLMN_HUMAN183-223411A:164-20441
1.7ENST000003081927ENSE00002185478chr6:161137677-161137795119PLMN_HUMAN223-263411A:204-24441
1.8ENST000003081928ENSE00002162125chr6:161139326-161139488163PLMN_HUMAN263-317551A:244-29855
1.9ENST000003081929ENSE00002174772chr6:161139725-161139870146PLMN_HUMAN317-366501A:298-33336
1.10ENST0000030819210ENSE00002171287chr6:161143440-161143599160PLMN_HUMAN366-419540--
1.11cENST0000030819211cENSE00002163078chr6:161152083-161152264182PLMN_HUMAN419-480620--
1.12bENST0000030819212bENSE00002160674chr6:161152777-161152925149PLMN_HUMAN480-529500--
1.13ENST0000030819213ENSE00002175196chr6:161155027-16115512094PLMN_HUMAN530-561320--
1.14ENST0000030819214ENSE00002152595chr6:161157919-161158039121PLMN_HUMAN561-601410--
1.15bENST0000030819215bENSE00002177616chr6:161159570-16115964475PLMN_HUMAN601-626260--
1.16ENST0000030819216ENSE00002172545chr6:161160100-161160240141PLMN_HUMAN626-673480--
1.17bENST0000030819217bENSE00002178747chr6:161162343-161162449107PLMN_HUMAN673-709370--
1.18bENST0000030819218bENSE00002181703chr6:161173147-161173292146PLMN_HUMAN709-757490--
1.19bENST0000030819219bENSE00001864790chr6:161173932-161174338407PLMN_HUMAN758-810530--

(-) 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:253
 aligned with PLMN_HUMAN | P00747 from UniProtKB/Swiss-Prot  Length:810

    Alignment length:253
                                   109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349   
           PLMN_HUMAN   100 LSECKTGNGKNYRGTMSKTKNGITCQKWSSTSPHRPRFSPATHPSEGLEENYCRNPDNDPQGPWCYTTDPEKRYDYCDILECEEECMHCSGENYDGKISKTMSGLECQAWDSQSPHAHGYIPSKFPNKNLKKNYCRNPDRELRPWCFTTDPNKRWELCDIPRCTTPPPSSGPTYQCLKGTGENYRGNVAVTVSGHTCQHWSAQTPHTHNRTPENFPCKNLDENYCRNPDGKRAPWCHTTNSQVRWEYCKIPSC 352
               SCOP domains d1ki0a1 A:81-163 Plasminogen                                                       d1ki0a2 A:164-250 Plasminogen                                                          d1ki0a3 A:251-333 Plasminogen                                                       SCOP domains
               CATH domains 1ki0A01 A:81-162 Plasminogen Kringle 4                                            1ki0A02 A:163-250 Plasminogen Kringle 4                                                 1ki0A03 A:251-333 Plasminogen Kringle 4                                             CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Kringle-1ki0A01 A:256-333                                                      Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Kringle-1ki0A02 A:256-333                                                      Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Kringle-1ki0A03 A:256-333                                                      Pfam domains (3)
         Sec.struct. author ...............................................................eee.......eee....................................................................eee.......eee.........................................................hhhhh...............eee.......eee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------QK------------P---------------------------------------------------------------------------------------H-------------------------H------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --KRINGLE_2  PDB: A:83-162 UniProt: 102-181                                       --KRINGLE_2  PDB: A:165-243 UniProt: 184-262                                     -----------KRINGLE_2  PDB: A:255-333 UniProt: 274-352                                      PROSITE (1)
                PROSITE (2) ---------------------------------------------------KRINGLE_1     --------------------------------------------------------------------KRINGLE_1    -----------------------------------------------------------------------------KRINGLE_1    ----------------- PROSITE (2)
           Transcript 1 (1) Exon 1.4a  PDB: A:81-117 [INCOMPLETE]----------------------------------------------Exon 1.6  PDB: A:164-204 UniProt: 183-223---------------------------------------Exon 1.8  PDB: A:244-298 UniProt: 263-317              ----------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.5b  PDB: A:117-164 UniProt: 136-183      ---------------------------------------Exon 1.7  PDB: A:204-244 UniProt: 223-263-----------------------------------------------------Exon 1.9  PDB: A:298-333             Transcript 1 (2)
                 1ki0 A  81 LSECKTGNGKNYRGTMSKTKNGITCQKWSSTSPHRPRFSPATHPSEGLEENYCRNPDNDPQGPWCYTTDPEKRYDYCDILECEEECMHCSGENYDGKISKTMSGLECQAWDSQSPHAHGYIPSKFPNKNLKKNYCRNPDRELRPWCFTTDPNKRWELCDIPRCTTPPPSSGPTYQCLKGTGENYRGNVAVTVSGHTCQHWSAQTPHTHERTPENFPCKNLDENYCRNPDGKRAPWCHTTNSQVRWEYCKIPSC 333
                                    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   

   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, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PLMN_HUMAN | P00747)
molecular function
    GO:0034185    apolipoprotein binding    Interacting selectively and non-covalently with an apolipoprotein, the protein component of a lipoprotein complex.
    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: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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    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:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    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:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:2000048    negative regulation of cell-cell adhesion mediated by cadherin    Any process that stops, prevents, or reduces the frequency, rate or extent of cell-cell adhesion mediated by cadherin.
    GO:0010812    negative regulation of cell-substrate adhesion    Any process that decreases the frequency, rate or extent of cell-substrate adhesion. Cell-substrate adhesion is the attachment of a cell to the underlying substrate via adhesion molecules.
    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:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0051919    positive regulation of fibrinolysis    Any process that activates, maintains or increases the frequency, rate or extent of fibrinolysis, an ongoing process that solubilizes fibrin, resulting in the removal of small blood clots.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0048771    tissue remodeling    The reorganization or renovation of existing tissues. This process can either change the characteristics of a tissue such as in blood vessel remodeling, or result in the dynamic equilibrium of a tissue such as in bone remodeling.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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.
    GO:0031232    extrinsic component of external side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its external surface, but not integrated into the hydrophobic region.
    GO:0044218    other organism cell membrane    The cell membrane of a secondary organism with which the first organism is interacting.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0031093    platelet alpha granule lumen    The volume enclosed by the membrane of the platelet alpha granule.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PLMN_HUMAN | P007471b2i 1bml 1bui 1cea 1ceb 1ddj 1hpj 1hpk 1i5k 1krn 1l4d 1l4z 1pk4 1pkr 1pmk 1qrz 1rjx 2doh 2doi 2knf 2l0s 2pk4 3uir 4a5t 4cik 4dcb 4dur 4duu 5hpg 5ugd 5ugg

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1KI0)