Apoptotic Protease-Activating Factor 1

(All numbering and residues are taken from first PDB file)

Run Details Domains Sequence Morph Domain Pairs Contact Graph

DynDom run details

  Property   Value
  Name Apoptotic Protease-Activating Factor 1
  Conformer 1
(PDB)
5wve (A)
  Conformer 2
(PDB)
3sfz (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 571 2.99   353 - 603   921 - 1246
2 243 1.41   107 - 349
3 309 1.81   604 - 920

Sequence


           ________________________________________________________________________________________________________________________ 
 5wve(A) : ***GITSYVRTVLCEGGVPQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIE 
         :                                                                                                                          
 3sfz(A) : TDGGITSFVRTVLCEGGVPQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIE 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 5wve(A) : EAKDRLRILMLRKHPRSLLILDDVWDSWVLKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYY 
         :                                                                                                                          
 3sfz(A) : EAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAFDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMKKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAYY 
           ________________________________________________________________________________________________________________________ 

           __346___________________________________________________________________________________________________________________ 
 5wve(A) : LKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMETEEVEDILQEFVNKSLLFCDRNGKSFRYYLHDLQVDFLTEKNCSQLQDLHKKII 
         :                                                                                                                          
 3sfz(A) : LRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLETEEVEDILQEFVNKSLLFCNRNGKSFCYYLHDLQVDFLTEKNRSQLQDLHRKMV 
           __346___________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 5wve(A) : TQFQRYHQPHTLSPDQEDCMYWYNFLAYHMASAKMHKELCALMFSLDWIKAKTELVGPAHLIHEFVEYRHILDEKDCAVSENFQEFLSLNGHLLGRQPFPNIVQLGLCEPETSEVYQQAK 
         :                                                                                                                          
 3sfz(A) : TQFQRYYQPHTLSPDQEDCMYWYNFLAYHMASANMHKELCALMFSLDWIKAKTELVGPAHLIHEFVAYRHILDEKDCAVCENFQEFLSLNGHLLGRQPFPNIVQLGLCEPETSEVYRQAK 
           ________________________________________________________________________________________________________________________ 

           ___________________603__________________________________________________________________________________________________ 
 5wve(A) : LQAKQEVDNGMLYLEWINKKNITNLSRLVVRPHTDAVYHACFSEDGQRIASCGADKTLQVFKAETGEKLLEIKAHEDEVLCCAFSTDDRFIATCSVDKKVKIWNSMTGELVHTYDEHSEQ 
         :                                                                                                                          
 3sfz(A) : LQAKQEGDTGRLYLEWINKKTIKNLSRLVVRPHTDAVYHACFSQDGQRIASCGADKTLQVFKAETGEKLLDIKAHEDEVLCCAFSSDDSYIATCSADKKVKIWDSATGKLVHTYDEHSEQ 
           ___________________603__________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 5wve(A) : VNCCHFTNSSHHLLLATGSSDCFLKLWDLNQKECRNTMFGHTNSVNHCRFSPDDKLLASCSADGTLKLWDATSANERKSINVKQFFLNLEDPQEDMEVIVKCCSWSADGARIMVAAKNKI 
         :                                                                                                                          
 3sfz(A) : VNCCHFTNKSNHLLLATGSNDFFLKLWDLNQKECRNTMFGHTNSVNHCRFSPDDELLASCSADGTLRLWDVRSANERKSINVKRFF--------dVEVIVKCCSWSADGDKIIVAAKNKV 
           ________________________________________________________________________________________________________________________ 

           ______________________________________________________________________________________________918_______________________ 
 5wve(A) : FLFDIHTSGLLGEIHTGHHSTIQYCDFSPQNHLAVVALSQYCVELWNTDSRSKVADCRGHLSWVHGVMFSPDGSSFLTSSDDQTIRLWETKKVCKNSAVMLKQEVDVVFQENEVMVLAVD 
         :                                                                                                                          
 3sfz(A) : LLFDIHTSGLLAEIHTGHHSTIQYCDFSPYDHLAVIALSQYCVELWNIDSRLKVADCRGHLSWVHGVMFSPDGSSFLTASDDQTIRVWETKKVCKNSAIVLKQEIDVVFQENETMVLAVD 
           ______________________________________________________________________________________________918_______________________ 

           ________________________________________________________________________________________________________________________ 
 5wve(A) : HIRRLQLINGRTGQIDYLTEAQVSCCCLSPHLQYIAFGDENGAIEILELVNNRIFQSRFQHKKTVWHIQFTADEKTLISSSDDAEIQVWNWQLDKCIFLRGHQETVKDFRLLKNSRLLSW 
         :                                                                                                                          
 3sfz(A) : NIRGLQLIAGKTGQIDYLPEAQVSCCCLSPHLEYVAFGDEDGAIKIIELPNNRVFSSGVGHKKAVRHIQFTADGKTLISSSEDSVIQVWNWQTGDYVFLQAHQETVKDFRLLQDSRLLSW 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 5wve(A) : SFDGTVKVWNIITGNKEKDFVCHQGTVLSCDISHDATKFSSTSADKTAKIWSFDLLLPLHELRGHNGCVRCSAFSVDSTLLATGDDNGEIRIWNVSNGELLHLCAPLSEEGAATHGGWVT 
         :                                                                                                                          
 3sfz(A) : SFDGTVKVWNVITGRIERDFTCHQGTVLSCAISSDATKFSSTSADKTAKIWSFDLLSPLHELKGHNGCVRCSAFSLDGILLATGDDNGEIRIWNVSDGQLLHSCAPIS------hGGWVT 
           ________________________________________________________________________________________________________________________ 

           ___________________________________________________________________                                                      
 5wve(A) : DLCFSPDGKMLISAGGYIKWWNVVTGESSQTFYTNGTNLKKIHVSPDFKTYVTVDNLGILYILQTLE                                                      
         :                                                                                                                          
 3sfz(A) : DVCFSPDSKTLVSAGGYLKWWNVATGDSSQTFYTNGTNLKKIHVSPDFRTYVTVDNLGILYILQVLE                                                      
           ___________________________________________________________________                                                      

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
142.7
Translation
(A)
-4.8
Closure
(%)
98.1
Bending Residues
( green )
  346 - 365
Bending Region Analysis
Property Value
Fixed Domain
( blue )
1
Moving Domain
( yellow )
3
Rotation Angle
(deg)
56.1
Translation
(A)
-3.4
Closure
(%)
12.0
Bending Residues
( green )
  603 - 604
  918 - 921
Bending Region Analysis

Dynamic Contact Graph

Conformer 1 Contact:
Residue 1 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 1

Movement classification: Hinge

Conformer 1 Contact:
Residue 1 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 1

Movement classification: Hinge

PyMOL Script

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