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 VIIA IN COMPLEX WITH THE INHIBITOR (2R,15R)-2-[(1-AMINOISOQUINOLIN-6-YL)AMINO]-4,15,17-TRIMETHYL-7-[1-(1H-TETRAZOL-5-YL)CYCLOPROPYL]-13-OXA-4,11-DIAZATRICYCLO[14.2.2.1~6,10~]HENICOSA-1(18),6(21),7,9,16,19-HEXAENE-3,12-DIONE
 
Authors :  A. Wei
Date :  02 Aug 16  (Deposition) - 28 Sep 16  (Release) - 12 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Glycoprotein, Hydrolase, Serine Protease, Plasma, Blood Coagulation Factor, Protein Inhibitor Complex, Calcium-Binding, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. U. Ladziata, P. W. Glunz, Y. Zou, X. Zhang, W. Jiang, S. Jacutin-Porte, D. L. Cheney, A. Wei, J. M. Luettgen, T. M. Harper, P. C. Wong, D. Seiffert, R. R. Wexler, E. S. Priestley
Synthesis And P1' Sar Exploration Of Potent Macrocyclic Tissue Factor-Factor Viia Inhibitors.
Bioorg. Med. Chem. Lett. V. 26 5051 2016
PubMed-ID: 27612545  |  Reference-DOI: 10.1016/J.BMCL.2016.08.088

(-) Compounds

Molecule 1 - COAGULATION FACTOR VII (HEAVY CHAIN)
    Chains: H
    EC Number: 3.4.21.21
    Engineered: YES
    Expression System: CRICETINAE
    Expression System Taxid: 10026
    Gene: F7
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROCONVERTIN,SERUM PROTHROMBIN CONVERSION ACCELERATOR,SPCA
 
Molecule 2 - COAGULATION FACTOR VII (LIGHT CHAIN)
    Chains: L
    EC Number: 3.4.21.21
    Engineered: YES
    Expression System: CRICETINAE
    Expression System Taxid: 10026
    Gene: F7
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROCONVERTIN,SERUM PROTHROMBIN CONVERSION ACCELERATOR,SPCA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
170A1Ligand/Ion(2R,15R)-2-[(1-AMINOISOQUINOLIN-6-YL)AMINO]-4,15,17-TRIMETHYL-7-[1-(1H-TETRAZOL-5-YL)CYCLOPROPYL]-13-OXA-4,11-DIAZATRICYCLO[14.2.2.1~6,10~]HENICOSA-1(18),6(21),7,9,16,19-HEXAENE-3,12-DIONE
2CA1Ligand/IonCALCIUM ION
3GOL2Ligand/IonGLYCEROL
4SO44Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS H:57 , CYS H:58 , ASP H:60 , LYS H:60A , GLY H:97 , THR H:98 , THR H:99 , ASP H:189 , SER H:190 , LYS H:192 , SER H:195 , SER H:214 , TRP H:215 , GLY H:216 , GLN H:217 , GLY H:219 , CYS H:220 , GLY H:226 , HOH H:436 , HOH H:441 , HOH H:470 , HOH H:589binding site for residue 70A H 301
2AC2SOFTWAREGLU H:70 , ASP H:72 , GLU H:75 , GLU H:80 , HOH H:427 , HOH H:592binding site for residue CA H 302
3AC3SOFTWAREARG H:83 , ARG H:84 , HIS H:109 , GLN H:110binding site for residue SO4 H 303
4AC4SOFTWAREVAL H:35 , ASN H:37 , LYS H:60A , LYS H:60C , ASN H:60Dbinding site for residue SO4 H 304
5AC5SOFTWARESER H:170B , ILE H:176 , HIS H:224 , PHE H:225 , VAL H:227binding site for residue SO4 H 305
6AC6SOFTWAREILE H:47 , ASN H:48 , GLN H:239 , HOH H:403 , HOH H:406 , HOH H:446 , HOH H:586 , HIS L:115binding site for residue SO4 H 306
7AC7SOFTWAREPHE H:59 , TRP H:61 , PRO H:96 , ARG H:147 , HOH H:412 , HOH H:430 , HOH H:495binding site for residue GOL H 307
8AC8SOFTWAREVAL H:129G , PHE H:135 , HIS H:202 , HOH H:487 , HOH H:516 , HOH H:517 , HOH H:540binding site for residue GOL H 308

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:27
2H:42 -H:58
3H:122 -L:135
4H:168 -H:182
5H:191 -H:220
6L:91 -L:102
7L:98 -L:112
8L:114 -L:127

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe H:256 -Pro H:257

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L30)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L30)

(-) Exons   (0, 0)

(no "Exon" information available for 5L30)

(-) 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 H from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeee....eeeehhhhhh...hhh.eeeee............eeeeeeeeeee............eeeee................hhhhhhhhhhhh.eeeeee..............eeeeeeeehhhhhhhhh.........eeee.........hhhhh..eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhhh.......eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5l30 H   16 IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHDLSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERTLAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCLQQSRDSPNITEYMFCAGYSDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMRSEPRPGVLLRAPFP  257
                                    25        35|       46        56    ||||62        72        82        92       102       112       122      129C|||||  139       150       160       170|||||||178     | 187|      196       206       216|| |   226       236       246       256 
                                              35|                     60A|||                                                                  129A|||||||          147|                  170A||||||     184A 188A                           217| |                                     
                                               37                      60B||                                                                   129B||||||           149                   170B|||||                                          219 |                                     
                                                                        60C|                                                                    129C|||||                                  170C||||                                           221A                                     
                                                                         60D                                                                     129D||||                                   170G|||                                                                                    
                                                                                                                                                  129E|||                                    170H||                                                                                    
                                                                                                                                                   129F||                                     170I|                                                                                    
                                                                                                                                                    129G|                                       175                                                                                    
                                                                                                                                                      134                                                                                                                              


Chain L from PDB  Type:PROTEIN  Length:56
                                                                                         
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh..eeeee...eeeee....eee......eee........hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                5l30 L   89 LICVNENGGCEQYCSDHTGTKRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILEKR  144
                                    98       108       118       128       138
   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 5L30)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L30)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L30)

(-) Gene Ontology  (35, 35)

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
    70A  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ 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 ]
 
  Cis Peptide Bonds
    Phe H:256 - Pro H:257   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5l30
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  FA7_HUMAN | P08709
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.21
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  FA7_HUMAN | P08709
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        FA7_HUMAN | P08709: 1bf9 1cvw 1dan 1dva 1f7e 1f7m 1fak 1ff7 1ffm 1j9c 1jbu 1kli 1klj 1nl8 1o5d 1qfk 1w0y 1w2k 1w7x 1w8b 1wqv 1wss 1wtg 1wun 1wv7 1ygc 1z6j 2a2q 2aei 2aer 2b7d 2b8o 2bz6 2c4f 2ec9 2f9b 2fir 2flb 2flr 2puq 2zp0 2zwl 2zzu 3ela 3th2 3th3 3th4 4ibl 4ish 4isi 4jyu 4jyv 4jzd 4jze 4jzf 4na9 4ng9 4nga 4x8s 4x8t 4x8u 4x8v 4ylq 4yt6 4yt7 4z6a 4zma 4zxx 4zxy 5i46 5l2y 5l2z 5pa8 5pa9 5paa 5pab 5pac 5pae 5paf 5pag 5pai 5paj 5pak 5pam 5pan 5pao 5paq 5par 5pas 5pat 5pau 5pav 5paw 5pax 5pay 5pb0 5pb1 5pb2 5pb3 5pb4 5pb5 5pb6 5tqe 5tqf 5tqg 5u6j

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5L30)