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(-) Description

Title :  CRYSTAL STRUCTURE OF FACTOR VIIA IN COMPLEX WITH 1-[[3-[2-HYDROXY-3-(1H-PYRROLO[3,2-C]PYRIDIN-2-YL)PHENYL]PHENYL]METHYL]-3-PHENYLUREA
 
Authors :  M. Stihle, A. Mayweg, S. Roever, M. G. Rudolph
Date :  10 Nov 16  (Deposition) - 21 Jun 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
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 :  A. Mayweg, S. Roever, M. G. Rudolph
Crystal Structure Of A Factor Viia Complex
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - COAGULATION FACTOR VII HEAVY CHAIN
    Chains: H
    EC Number: 3.4.21.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    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: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    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  (6, 12)

Asymmetric/Biological Unit (6, 12)
No.NameCountTypeFull Name
17XD1Ligand/Ion1-[[3-[2-OXIDANYL-3-(1~{H}-PYRROLO[3,2-C]PYRIDIN-2-YL)PHENYL]PHENYL]METHYL]-3-PHENYL-UREA
2CA1Ligand/IonCALCIUM ION
3CL3Ligand/IonCHLORIDE ION
4GOL4Ligand/IonGLYCEROL
5MHO1Mod. Amino AcidS-OXYMETHIONINE
6SO42Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU H:25 , HIS H:41 , CYS H:42 , ASP H:44 , LYS H:45 , GLY H:85 , SER H:187 , CYS H:188 , LYS H:189 , SER H:192 , SER H:211 , TRP H:212 , GLY H:213 , GLY H:215 , GOL H:304 , HOH H:415 , HOH H:519binding site for residue 7XD H 301
02AC2SOFTWAREARG H:72 , HIS H:97binding site for residue CL H 302
03AC3SOFTWAREPHE H:43 , ASP H:44 , ARG H:138 , HOH H:451 , HOH H:475binding site for residue GOL H 303
04AC4SOFTWAREGLN H:24 , LEU H:25 , LYS H:189 , GLY H:190 , 7XD H:301 , HOH H:407 , HOH H:413 , HOH H:415binding site for residue GOL H 304
05AC5SOFTWAREHOH H:547binding site for residue GOL H 305
06AC6SOFTWAREGLU H:58 , ASP H:60 , GLU H:63 , GLU H:68 , HOH H:432 , HOH H:564binding site for residue CA H 306
07AC7SOFTWAREARG H:240binding site for residue CL H 307
08AC8SOFTWAREGLU H:242 , GOL L:201binding site for residue CL H 308
09AC9SOFTWAREMET H:154 , THR H:155 , ARG H:227 , HOH H:409 , HOH H:481binding site for residue SO4 H 309
10AD1SOFTWAREGLU H:242 , CL H:308 , CYS L:114 , SER L:119 , LEU L:120 , HOH L:308binding site for residue GOL L 201
11AD2SOFTWAREARG H:119 , CYS L:102 , SER L:103 , ASP L:104 , HOH L:314binding site for residue SO4 L 202

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1H:7 -H:12
2H:26 -H:42
3H:110 -L:135
4H:158 -H:177
5H:188 -H:216
6L:91 -L:102
7L:98 -L:112
8L:114 -L:127

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe H:253 -Pro H:254

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5PAB)

(-) 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:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee..eeeehhhhhh...hhh.eeeee............eeeeeeeeeee............eeeee................hhhhhhhhhhhh.eeeeee..............eeeeeeeehhhhhhhhh......eeee................eeeeee..eeeeeeee............eeeee...hhhhhhhhhh.......eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5pab H   1 IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHDLSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERTLAFVRFSLVSGWGQLLDRGATALELmVLNVPRLMTQDCLQQSRNITEYMFCAGYSDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMRSEPRPGVLLRAPFP 254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140     | 150       160  ||   176       186       196       206       216       226       236       246        
                                                                                                                                                                           146-MHO          163|                                                                                    
                                                                                                                                                                                             170                                                                                    


Chain L from PDB  Type:PROTEIN  Length:55
                                                                                       
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..eeeee...eeeee....eee......eee........hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                 5pab L  89 LICVNENGGCEQYCSDHTGTKRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILEK 143
                                    98       108       118       128       138
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 5PAB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (35, 35)

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 4ylq 4yt6 4yt7 4z6a 4zma 4zxx 4zxy 5i46 5l2y 5l2z 5l30 5pa8 5pa9 5paa 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

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