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(-) Description

Title :  CRYSTAL STRUCTURE OF A FVIIA-TRYPSIN CHIMERA (YT) IN COMPLEX WITH SOLUBLE TISSUE FACTOR
 
Authors :  A. B. Sorensen, L. A. Svensson, P. S. Gandhi
Date :  04 Apr 15  (Deposition) - 30 Dec 15  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  H,L,T
Keywords :  Trypsin-Fold, Protein-Protein Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. B. Sorensen, J. J. Madsen, L. A. Svensson, A. A. Pedersen, H. Stergaard, M. T. Overgaard, O. H. Olsen, P. S. Gandhi
Molecular Basis Of Enhanced Activity In Factor Viia-Trypsin Variants Conveys Insights Into Tissue Factor-Mediated Allosteric Regulation Of Factor Viia Activity.
J. Biol. Chem. V. 291 4671 2016
PubMed-ID: 26694616  |  Reference-DOI: 10.1074/JBC.M115.698613

(-) Compounds

Molecule 1 - COAGULATION FACTOR VII
    Chains: L
    EC Number: 3.4.21.21
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHOEBNALT85
    Expression System Common: CHINESE HAMSTER
    Expression System Plasmid: PQMCF-5
    Expression System Taxid: 10029
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 108-203
    Gene: F7
    Organ: KIDNEY
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROCONVERTIN,SERUM PROTHROMBIN CONVERSION ACCELERATOR,SPCA
    Tissue: BLOOD
 
Molecule 2 - COAGULATION FACTOR VII
    Chains: H
    EC Number: 3.4.21.21
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHOEBNALT85
    Expression System Common: CHINESE HAMSTER
    Expression System Plasmid: PQMCF-5
    Expression System Taxid: 10029
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 213-465
    Gene: F7
    Mutation: YES
    Organ: KIDNEY
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROCONVERTIN,SERUM PROTHROMBIN CONVERSION ACCELERATOR,SPCA
    Tissue: BLOOD
 
Molecule 3 - TISSUE FACTOR
    Chains: T
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Common: CHINESE HAMSTER
    Expression System Plasmid: PET3A
    Expression System Strain: ORIGAMI 2
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 36-242
    Gene: F3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TF,COAGULATION FACTOR III,THROMBOPLASTIN
    Tissue: BLOOD

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 5)

Asymmetric/Biological Unit (5, 5)
No.NameCountTypeFull Name
10Z61Ligand/IonD-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PHENYLALANINAMIDE
2BGC1Ligand/IonBETA-D-GLUCOSE
3CA1Ligand/IonCALCIUM ION
4CIT1Ligand/IonCITRIC ACID
5FUC1Ligand/IonALPHA-L-FUCOSE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN L:49 , SER L:52 , TYR L:68binding site for residue BGC L 201
2AC2SOFTWAREHIS H:57 , GLY H:97 , THR H:98 , ASP H:189 , SER H:190 , CYS H:191 , GLY H:193 , SER H:195 , SER H:214 , TRP H:215 , GLY H:216 , GLN H:217 , GLY H:218 , GLY H:226 , HOH H:630 , HOH H:644 , HOH H:681binding site for residue 0Z6 H 501
3AC3SOFTWAREGLU H:70 , ASP H:72 , GLU H:75 , GLU H:80 , HOH H:606 , HOH H:687binding site for residue CA H 502
4AC4SOFTWARELYS T:166 , ASP T:178 , ASP T:180 , TYR T:185binding site for residue CIT T 301
5AC5SOFTWAREGLY L:58 , SER L:60 , PHE L:71 , HOH L:319 , ARG T:131binding site for Mono-Saccharide FUC L 202 bound to SER L 60

(-) SS Bonds  (13, 13)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:27
2H:41 -H:58
3H:168 -H:182
4H:191 -H:219
5L:50 -L:61
6L:55 -L:70
7L:72 -L:81
8L:91 -L:102
9L:98 -L:112
10L:114 -L:127
11L:135 -H:122
12T:49 -T:57
13T:186 -T:209

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asp L:104 -His L:105
2Lys L:109 -Arg L:110
3Phe H:256 -Pro H:257
4Glu T:26 -Pro T:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z6A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z6A)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z6A)

(-) 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:249
                                                                                                                                                                                                                                                                                          
               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..............eeeeeeeehhhhhh..........eeee................eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhh........eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4z6a H   16 IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHDLSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERTLAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCEASYPGKITEYMFCAGYSDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMRSEPRPGVLLRAPFP  257
                                    25        35     || 46        56    ||||62        72        82        92       102       112       122      129C       139       150       160       170       180   |   188       198       208       218       228       238       248         
                                                    41|               60A|||                                                                  129A||               147|                               183A 187A                                                                      
                                                     43                60B||                                                                   129B|                149                                                                                                              
                                                                        60C|                                                                    129C                                                                                                                                 
                                                                         60D                                                                                                                                                                                                         


Chain L from PDB  Type:PROTEIN  Length:94
                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh......eeee....eeee....ee.....ee........hhhhhh..ee.......ee....eee......eee........hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                4z6a L   48 DQCASSPCQNGGSCKDQLQSYICFCLPAFEGRNCETHKDDQLICVNENGGCEQYCSDHTKRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILEK  143
                                    57        67        77        87        97       109       119       129       139    
                                                                                    106|                                  
                                                                                     109                                  


Chain T from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                          
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee..eeeeeee.....eeeeeeeee.....eeeeeee...eeehhhhhh......eeeeeeeee........eee....hhhhhh......eeeeeee..eeeeee...eeeeee..eeeehhhhhhhhheeeeeeee......eeeee...eeeee......eeeeeeee...............ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4z6a T    4 TNTVAAYNLTWKSTNFKTILEWEPKPVNQVYTVQISTKSGDWKSKCFYTTDTECDLTDEIVKDVKQTYLARVFSYPAGNVGEPLYENSPEFTPYLETNLGQPTIQSFEQVGTKVNVTVEDERTLVRRNNTFLSLRDVFGKDLIYTLYYWKSSSSGKKTAKTNTNEFLIDVDKGENYCFSVQAVIPSRTVNRKSTDSPVECM  210
                                    13        23        33        43        53        63        73        83|       99       109       119       129       139       149       159       169       179       189       199       209 
                                                                                                          83|                                                                                                                        
                                                                                                           90
   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 4Z6A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z6A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z6A)

(-) Gene Ontology  (61, 72)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asp L:104 - His L:105   [ RasMol ]  
    Glu T:26 - Pro T:27   [ RasMol ]  
    Lys L:109 - Arg L:110   [ RasMol ]  
    Phe H:256 - Pro H:257   [ RasMol ]  
 

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  3.4.21.21
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 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 4zma 4zxx 4zxy 5i46 5l2y 5l2z 5l30 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
        TF_HUMAN | P13726: 1ahw 1boy 1dan 1fak 1j9c 1jps 1nl8 1o5d 1tfh 1uj3 1w0y 1w2k 1wqv 1wss 1wtg 1wun 1wv7 1z6j 2a2q 2aei 2aer 2b7d 2b8o 2c4f 2cef 2ceh 2cez 2cfj 2ec9 2f9b 2fir 2flb 2flr 2hft 2puq 2zp0 2zwl 2zzu 3ela 3th2 3th3 3th4 4ibl 4m7l 4ylq 4zma 5w06

(-) Related Entries Specified in the PDB File

4ylq