Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  FACTOR XIA IN COMPLEX WITH THE INHIBITOR METHYL ((15S)-15-(((2E)-3-(5-CHLORO-2-(1H-TETRAZOL-1-YL)PHENYL)-2-PROPENOYL)AMINO)-9-OXO-8,17,19-TRIAZATRICYCLO[14.2.1.0~2,7~]NONADECA-1(18),2,4,6,16(19)-PENTAEN-5-YL)CARBAMATE
 
Authors :  S. Sheriff
Date :  07 Oct 16  (Deposition) - 01 Mar 17  (Release) - 01 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.12
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Serine Protease, Blood Coagulation Factor, Protein Inhibitor Complex, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Corte, T. Fang, H. Osuna, D. J. Pinto, K. A. Rossi, J. E. Myers, S. Sheriff, Z. Lou, J. J. Zheng, T. W. Harper, J. M. Bozarth, Y. Wu, J. M. Luettgen, D. A. Seiffert, C. P. Decicco, R. R. Wexler, M. L. Quan
Structure-Based Design Of Macrocyclic Factor Xia Inhibitors Discovery Of The Macrocyclic Amide Linker.
J. Med. Chem. V. 60 1060 2017
PubMed-ID: 28085275  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01460
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FACTOR XIA (LIGHT CHAIN)
    ChainsA
    EC Number3.4.21.27
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET14B
    Expression System StrainDE3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneF11
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFXI,PLASMA THROMBOPLASTIN ANTECEDENT,PTA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
17DK1Ligand/IonMETHYL ((15S)-15-(((2E)-3-(5-CHLORO-2-(1H-TETRAZOL-1-YL)PHENYL)-2-PROPENOYL)AMINO)-9-OXO-8,17,19-TRIAZATRICYCLO[14.2.1.0~2,7~]NONADECA-1(18),2,4,6,16(19)-PENTAEN-5-YL)CARBAMATE
2EDO10Ligand/Ion1,2-ETHANEDIOL
3SO42Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:39 , HIS A:40 , LEU A:41 , HIS A:57 , LEU A:147 , ILE A:151 , ASP A:189 , ALA A:190 , CYS A:191 , LYS A:192 , GLY A:193 , ASP A:194 , SER A:195 , TRP A:215 , GLY A:216 , GLY A:218 , CYS A:219 , GLY A:226 , VAL A:227 , EDO A:304 , EDO A:306 , HOH A:465 , HOH A:476 , HOH A:522binding site for residue 7DK A 301
02AC2SOFTWAREVAL A:23 , ARG A:24 , GLY A:25 , GLU A:26 , TRP A:27 , PRO A:28 , ILE A:70 , LEU A:71 , LEU A:155 , HOH A:410 , HOH A:457binding site for residue SO4 A 302
03AC3SOFTWAREARG A:170 , ARG A:184Bbinding site for residue SO4 A 303
04AC4SOFTWARE7DK A:301 , EDO A:306 , EDO A:307 , HOH A:566binding site for residue EDO A 304
05AC5SOFTWAREASN A:49 , THR A:111 , VAL A:112 , GLY A:113 , TYR A:114binding site for residue EDO A 305
06AC6SOFTWARESER A:81 , LEU A:147 , GLY A:216 , GLU A:217 , GLY A:218 , 7DK A:301 , EDO A:304 , EDO A:307 , HOH A:514binding site for residue EDO A 306
07AC7SOFTWAREGLY A:216 , GLU A:217 , EDO A:304 , EDO A:306 , HOH A:458 , HOH A:558binding site for residue EDO A 307
08AC8SOFTWAREHIS A:178binding site for residue EDO A 308
09AC9SOFTWAREGLN A:38 , ILE A:76 , LYS A:77 , HOH A:415binding site for residue EDO A 309
10AD1SOFTWAREHIS A:178 , MET A:180 , ILE A:181 , ASN A:230 , HOH A:430 , HOH A:464binding site for residue EDO A 310
11AD2SOFTWARESER A:99 , GLY A:100 , TYR A:101 , THR A:177 , LYS A:179binding site for residue EDO A 311
12AD3SOFTWAREGLU A:26 , TRP A:137 , LYS A:157 , HOH A:419binding site for residue EDO A 312
13AD4SOFTWAREILE A:47 , GLY A:48 , THR A:242 , GLN A:243 , HOH A:436binding site for residue EDO A 313

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:58
2A:136 -A:201
3A:168 -A:182
4A:191 -A:219

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:36A-Pro A:36B

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TKU)

(-) 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:238
                                                                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee.....eeeeeeeeee..eeeehhhhhh...hhh.eeee....hhhhh......eeeeeeee.....hhhhh...eeeee................hhhhhhh....eeeee..............eeee..eehhhhhhhhh........eeee................eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5tku A   16 IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVGYGDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV  245
                                    25        35 ||     43        53     || 61    ||  69        79        89        99       109       119       129       139   ||  150       160       169       179     ||187       197       207       217       227       237        
                                               36A|                    58A|     65A|                                                                           143|                    168A             184A|                                                             
                                                36B                     58B      65B                                                                            145                                      184B                                                             

   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 5TKU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    7DK  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:36A - Pro A:36B  [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5tku
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  FA11_HUMAN | P03951
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.27
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  FA11_HUMAN | P03951
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        FA11_HUMAN | P039511xx9 1xxd 1xxf 1zhm 1zhp 1zhr 1zjd 1zlr 1zmj 1zml 1zmn 1zom 1zpb 1zpc 1zpz 1zrk 1zsj 1zsk 1zsl 1ztj 1ztk 1ztl 2f83 2fda 2j8j 2j8l 3bg8 3sor 3sos 4cr5 4cr9 4cra 4crb 4crc 4crd 4cre 4crf 4crg 4d76 4d7f 4d7g 4na7 4na8 4ty6 4ty7 4wxi 4x6m 4x6n 4x6o 4x6p 4y8x 4y8y 4y8z 5e2o 5e2p 5eod 5eok 5exl 5exm 5exn 5i25 5q0d 5q0e 5q0f 5q0g 5q0h 5tks 5tkt

(-) Related Entries Specified in the PDB File

5tks 5tkt