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 XA COMPLEX WITH GTC000422
 
Authors :  M. A. Convery, R. J. Young, S. Senger, J. N. Hamblin, C. Chan, J. R. Toomey N. S. Watson
Date :  13 Feb 15  (Deposition) - 30 Sep 15  (Release) - 30 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Convery, R. J. Young, S. Senger, J. N. Hamblin, C. Chan, J. R. Toomey, N. S. Watson
Factor Xa Complex With Gtc000422
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COAGULATION FACTOR X
    Chains: A
    EC Number: 3.4.21.6
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: STUART FACTOR,STUART-PROWER FACTOR, ACTIVATED FACTOR XA HEAVY CHAIN
 
Molecule 2 - COAGULATION FACTOR X
    Chains: B
    EC Number: 3.4.21.6
    Fragment: UNP RESIDUES 46-179
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: STUART FACTOR,STUART-PROWER FACTOR, FACTOR X LIGHT CHAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
19871Ligand/IonN-[(3S)-1-{(2S)-1-[(3S)-3-AMINOPIPERIDIN-1-YL]-1-OXOPROPAN-2-YL}-2-OXOPYRROLIDIN-3-YL]-6-CHLORONAPHTHALENE-2-SULFONAMIDE
2CA1Ligand/IonCALCIUM ION
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:70 , ASN A:72 , GLN A:75 , GLU A:80 , HOH A:459 , HOH A:485 , HOH A:518binding site for residue CA A 301
2AC2SOFTWARETYR A:185 , ASP A:185A , ARG A:222 , LYS A:224 , HOH A:526binding site for residue MG A 302
3AC3SOFTWARELYS A:96 , GLU A:97 , PHE A:174 , ASP A:189 , ALA A:190 , GLN A:192 , SER A:195 , VAL A:213 , TRP A:215 , GLY A:216 , GLY A:219 , GLY A:226 , ILE A:227 , TYR A:228 , HOH A:515 , HOH A:551binding site for residue 987 A 303

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:27
2A:42 -A:58
3A:122 -B:44
4A:168 -A:182
5A:191 -A:220
6B:1 -B:12
7B:8 -B:21
8B:23 -B:36

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Y7A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y7A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y7A)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y7A)

(-) 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:234
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........eeeee.....eeeeeee....eeeehhhhhhh....eeee............eee.eeeeee.............eeeee................hhhhhhhhh....eeeeee..............eeeeee..hhhhhhhhh.......eeee................eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4y7a A   16 IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKT  244
                                    25        35        45        55      | 64        74        84        94       104       114      124A       131       141   ||  152       162       172       182   ||  190       200       210      |221  |    230       240    
                                                                        61A                                                           124A    131A|            145|                                   185A|                             217| 223A                     
                                                                                                                                               131B             147                                    185B                              219                          


Chain B from PDB  Type:PROTEIN  Length:53
                                                                                      
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..eeee....eeee....eee......eee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                4y7a B   -2 RKLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTLE   50
                                     7        17        27        37        47
   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 4Y7A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y7A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y7A)

(-) Gene Ontology  (22, 22)

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
    987  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4y7a)
 

(-) 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
  4y7a
    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
  FA10_HUMAN | P00742
    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)
  3.4.21.6
    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
  FA10_HUMAN | P00742
    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
        FA10_HUMAN | P00742: 1c5m 1ezq 1f0r 1f0s 1fax 1fjs 1fxy 1g2l 1g2m 1hcg 1ioe 1iqe 1iqf 1iqg 1iqh 1iqi 1iqj 1iqk 1iql 1iqm 1iqn 1ksn 1lpg 1lpk 1lpz 1lqd 1mq5 1mq6 1msx 1nfu 1nfw 1nfx 1nfy 1nl8 1p0s 1v3x 1wu1 1xka 1xkb 1z6e 2bmg 2boh 2bok 2bq6 2bq7 2bqw 2cji 2d1j 2ei6 2ei7 2ei8 2fzz 2g00 2gd4 2h9e 2j2u 2j34 2j38 2j4i 2j94 2j95 2jkh 2p16 2p3f 2p3t 2p3u 2p93 2p94 2p95 2phb 2pr3 2q1j 2ra0 2uwl 2uwo 2uwp 2vh0 2vh6 2vvc 2vvu 2vvv 2vwl 2vwm 2vwn 2vwo 2w26 2w3i 2w3k 2wyg 2wyj 2xbv 2xbw 2xbx 2xby 2xc0 2xc4 2xc5 2y5f 2y5g 2y5h 2y7x 2y7z 2y80 2y81 2y82 3cen 3cs7 3ens 3ffg 3hpt 3iit 3k9x 3kl6 3kqb 3kqc 3kqd 3kqe 3liw 3m36 3m37 3q3k 3sw2 3tk5 3tk6 4a7i 4bti 4btt 4btu 4y6d 4y71 4y76 4y79 4y7b 4zh8 4zha 5jqy 5jtc 5jz8 5jzu 5k0h

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4Y7A)