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(-) Description

Title :  CRYSTAL STRUCTURE OF A FVIIA-TRYPSIN CHIMERA (FT) IN COMPLEX WITH SOLUBLE TISSUE FACTOR
 
Authors :  A. B. Sorensen, L. A. Svensson, P. S. Gandhi
Date :  05 Mar 15  (Deposition) - 30 Dec 15  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
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: BLOOD COAGULATION FACTOR VIIA LIGHT CHAIN, UNP RESIDUES 61- 212
    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 213-466
    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 Plasmid: PET3A
    Expression System Taxid: 469008
    Expression System Variant: ORIGAMI 2
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 33-251
    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  (8, 47)

Asymmetric/Biological Unit (8, 47)
No.NameCountTypeFull Name
10Z71Ligand/IonN-ACETYL-D-PHENYLALANYL-N-[(2S,3S)-6-CARBAMIMIDAMIDO-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PHENYLALANINAMIDE
2BGC1Ligand/IonBETA-D-GLUCOSE
3CA9Ligand/IonCALCIUM ION
4CGU10Mod. Amino AcidGAMMA-CARBOXY-GLUTAMIC ACID
5FUC1Ligand/IonALPHA-L-FUCOSE
6POL1Ligand/IonN-PROPANOL
7TMA22Ligand/IonTETRAMETHYLAMMONIUM ION
8XYS2Ligand/IonXYLOPYRANOSE

(-) Sites  (35, 35)

Asymmetric Unit (35, 35)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP L:46 , GLY L:47 , GLN L:49 , ASP L:63 , GLN L:64 , HOH L:391binding site for residue CA L 201
02AC2SOFTWARECGU L:7 , CGU L:26 , CGU L:29 , HOH L:334 , HOH L:414binding site for residue CA L 202
03AC3SOFTWARECGU L:7 , CGU L:16 , CGU L:26 , CGU L:29 , CA L:204 , HOH L:324 , HOH L:377 , HOH L:413binding site for residue CA L 203
04AC4SOFTWAREALA L:1 , ASN L:2 , CGU L:6 , CGU L:7 , CGU L:16 , CGU L:26 , CA L:203binding site for residue CA L 204
05AC5SOFTWAREALA L:1 , CGU L:6 , CGU L:16 , CGU L:20 , HOH L:415binding site for residue CA L 205
06AC6SOFTWARECGU L:20 , HOH L:343 , HOH L:349 , HOH L:405 , HOH L:419binding site for residue CA L 206
07AC7SOFTWARECGU L:14 , CGU L:19binding site for residue CA L 207
08AC8SOFTWARECGU L:25 , CGU L:29 , HOH L:303 , HOH L:394 , HOH L:407binding site for residue CA L 208
09AC9SOFTWAREGLY H:205 , HOH H:754 , ARG L:9 , GLU L:142binding site for residue TMA L 213
10AD1SOFTWAREHIS H:57 , GLY H:97 , THR H:98 , THR H:99 , ASP H:102 , ASP H:189 , SER H:190 , CYS H:191 , LYS H:192 , GLY H:193 , SER H:195 , SER H:214 , TRP H:215 , GLY H:216 , GLY H:218 , GLY H:226 , HOH H:630 , HOH H:656 , HOH H:694 , HOH H:773binding site for residue 0Z7 H 501
11AD2SOFTWAREGLU H:70 , ASP H:72 , GLU H:75 , GLU H:80 , HOH H:602 , HOH H:648 , HOH H:757binding site for residue CA H 502
12AD3SOFTWAREHIS H:76 , SER H:82 , PHE H:256 , HOH H:655 , HOH H:811binding site for residue TMA H 503
13AD4SOFTWAREHIS H:76 , HOH H:612 , PRO T:194binding site for residue TMA H 504
14AD5SOFTWAREGLU T:84binding site for residue TMA H 505
15AD6SOFTWAREPHE H:135 , ASN H:159binding site for residue TMA H 506
16AD7SOFTWAREHOH H:746binding site for residue TMA H 507
17AD8SOFTWARETRP H:215binding site for residue TMA H 508
18AD9SOFTWAREHIS H:224 , HOH H:731 , ASP L:87 , LEU L:89binding site for residue POL H 509
19AE1SOFTWAREHIS H:202 , HOH H:728 , HOH H:784 , CGU L:7binding site for residue TMA H 510
20AE2SOFTWAREGLN H:166 , ASP H:167 , HOH H:609 , GLY L:107 , TYR T:94 , GLU T:95 , ASN T:96binding site for residue TMA H 511
21AE3SOFTWAREGLY H:97 , THR H:98 , HOH H:769binding site for residue TMA H 512
22AE4SOFTWAREHOH H:775 , GLU T:174 , PHE T:175 , LEU T:176 , HOH T:412 , HOH T:548binding site for residue TMA T 301
23AE5SOFTWAREPHE H:132 , SER T:47 , TYR T:78binding site for residue TMA T 302
24AE6SOFTWARELYS T:68 , VAL T:146 , PHE T:147binding site for residue TMA T 303
25AE7SOFTWARETYR T:10 , GLU T:26 , GLN T:114 , SER T:115binding site for residue TMA T 304
26AE8SOFTWARELYS L:62 , ASP L:63 , GLN T:110 , THR T:112 , PRO T:206binding site for residue TMA T 305
27AE9SOFTWAREILE L:69 , XYS L:211 , HOH L:302 , LYS T:15 , THR T:17 , LYS T:20binding site for residue TMA T 306
28AF1SOFTWAREHOH L:339 , SER T:160 , ASN T:184binding site for residue TMA T 307
29AF2SOFTWARESER T:97 , HOH T:506binding site for residue TMA T 308
30AF3SOFTWARETYR T:156 , LYS T:165 , ASP T:204binding site for residue TMA T 309
31AF4SOFTWARELYS T:41 , HOH T:569binding site for residue TMA T 310
32AF5SOFTWARELEU T:12 , THR T:13binding site for residue TMA T 311
33AF6SOFTWAREASP H:146 , CYS H:219 , THR H:221 , THR T:52 , THR T:53 , ASP T:54binding site for residue TMA T 312
34AF7SOFTWAREGLN L:49 , SER L:52 , GLN L:66 , SER L:67 , TYR L:68 , ARG L:79 , HOH L:302 , HOH L:306 , HOH L:399 , TMA T:306 , HOH T:409binding site for Poly-Saccharide residues BGC L 209 through XYS L 211 bound to SER L 52
35AF8SOFTWAREGLY L:58 , SER L:60 , HOH L:308 , HOH L:326binding site for Mono-Saccharide FUC L 212 bound to SER L 60

(-) SS Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:27
2H:41 -H:58
3H:168 -H:182
4H:191 -H:219
5L:17 -L:22
6L:50 -L:61
7L:55 -L:70
8L:72 -L:81
9L:91 -L:102
10L:98 -L:112
11L:114 -L:127
12L:135 -H:122
13T:49 -T:57
14T:186 -T:209

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe H:256 -Pro H:257
2Glu T:26 -Pro T:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YLQ)

(-) 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...hhhhhhhhhhh......eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ylq H   16 IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHDLSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERTLAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCEASFPGKITEYMFCAGYSDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMRSEPRPGVLLRAPFP  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:143
                                                                                                                                                                                
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..............eeeee..eeeee....ee.....ee........hhhhhh..eeeee..eeeeee....eee......eee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ylq L    1 ANAFLeeLRPGSLeReCKeeQCSFeeAReIFKDAeRTKLFWISYSDGDQCASSPCQNGGSCKDQLQSYICFCLPAFEGRNCETHKDDQLICVNENGGCEQYCSDHTGTKRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILEK  143
                                 || 10   | |  20    ||  30    |   40        50        60        70        80        90       100       110       120       130       140   
                                 6-CGU  14-CGU||    ||  |     |                                                                                                            
                                  7-CGU   16-CGU    ||  |     |                                                                                                            
                                             19-CGU ||  |     |                                                                                                            
                                              20-CGU||  |     |                                                                                                            
                                                   25-CGU     |                                                                                                            
                                                    26-CGU    |                                                                                                            
                                                       29-CGU |                                                                                                            
                                                             35-CGU                                                                                                        


Chain T from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               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
                4ylq T    1 SGTTNTVAAYNLTWKSTNFKTILEWEPKPVNQVYTVQISTKSGDWKSKCFYTTDTECDLTDEIVKDVKQTYLARVFSYPAGNVESTGSAGEPLYENSPEFTPYLETNLGQPTIQSFEQVGTKVNVTVEDERTLVRRNNTFLSLRDVFGKDLIYTLYYWKSSSSGKKTAKTNTNEFLIDVDKGENYCFSVQAVIPSRTVNRKSTDSPVECM  210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 4YLQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (61, 72)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4yt6 4yt7 4z6a 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 4z6a 4zma 5w06

(-) Related Entries Specified in the PDB File

4z6a CONTAINS A RELATED FVIIA-TRYPSIN 170 LOOP CHIMERA.