DynDom - Protein Domain Motions

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)	1z6t (A)
Conformer 2 (PDB)	3jbt (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	244	1.59	107 - 350
2	234	3.17	351 - 584

Sequence

`________________________________________________________________________________________________________________________` `1z6t(A) : MDAKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMILKKDNDSYVSFYNALLHEGYKDLAALLHDGIPVVgITSYVRTVLCEGGVPQRPVVFVTRK` `:` `3jbt(A) : ********************************************************************************************GITSYVRTVLCEGGVPQRPVVFVTRK` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1z6t(A) : KLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWV` `:` `3jbt(A) : KLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSWV` `________________________________________________________________________________________________________________________` `_____________________________________________________________________________________________346________________________` `1z6t(A) : LKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSI` `:` `3jbt(A) : LKAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSI` `_____________________________________________________________________________________________346________________________` `________________________________________________________________________________________________________________________` `1z6t(A) : SVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMETEEVEDILQEFVNKSLLFCDRNGKSFRYYLHDLQVDFLTEKNCSQLQDLHKKIITQFQRYHQPHTLSPDQEDCMYWYNFLAYH` `:` `3jbt(A) : SVEMLREDIKDYYTDLSILQKDVKVPTKVLCILWDMETEEVEDILQEFVNKSLLFCDRNGKSFRYYLHDLQVDFLTEKNCSQLQDLHKKIITQFQRYHQPHTLSPDQEDCMYWYNFLAYH` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1z6t(A) : MASAKMHKELCALMFSLDWIKAKTELVGPAHLIHEFVEYRHILDEKDCAVSENFQEFLSLNGHLLGRQPFPNIVQLGLCEPETSEVYQQAKLQAKQ********************` `:` `3jbt(A) : MASAKMHKELCALMFSLDWIKAKTELVGPAHLIHEFVEYRHILDEKDCAVSENFQEFLSLNGHLLGRQPFPNIVQLGLCEPETSEVYQQAKLQAKQEVDNGMLYLEWINKKNITNLSRLV` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1z6t(A) : ********************************************************************************************************************` `:` `3jbt(A) : VRPHTDAVYHACFSEDGQRIASCGADKTLQVFKAETGEKLLEIKAHEDEVLCCAFSTDDRFIATCSVDKKVKIWNSMTGELVHTYDEHSEQVNCCHFTNSSHHLLLATGSSDCFLKLWDL` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1z6t(A) : ********************************************************************************************************************` `:` `3jbt(A) : NQKECRNTMFGHTNSVNHCRFSPDDKLLASCSADGTLKLWDATSANERKSINVKQFFLNLEDPQEDMEVIVKCCSWSADGARIMVAAKNKIFLFDIHTSGLLGEIHTGHHSTIQYCDFSP` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1z6t(A) : ********************************************************************************************************************` `:` `3jbt(A) : QNHLAVVALSQYCVELWNTDSRSKVADCRGHLSWVHGVMFSPDGSSFLTSSDDQTIRLWETKKVCKNSAVMLKQEVDVVFQENEVMVLAVDHIRRLQLINGRTGQIDYLTEAQVSCCCLS` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1z6t(A) : ********************************************************************************************************************` `:` `3jbt(A) : PHLQYIAFGDENGAIEILELVNNRIFQSRFQHKKTVWHIQFTADEKTLISSSDDAEIQVWNWQLDKCIFLRGHQETVKDFRLLKNSRLLSWSFDGTVKVWNIITGNKEKDFVCHQGTVLS` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1z6t(A) : ********************************************************************************************************************` `:` `3jbt(A) : CDISHDATKFSSTSADKTAKIWSFDLLLPLHELRGHNGCVRCSAFSVDSTLLATGDDNGEIRIWNVSNGELLHLCAPLSEEGAATHGGWVTDLCFSPDGKMLISAGGYIKWWNVVTGESS` `________________________________________________________________________________________________________________________` `______________________________________` `1z6t(A) : ************************************` `:` `3jbt(A) : QTFYTNGTNLKKIHVSPDFKTYVTVDNLGILYILQTLE` `______________________________________`

Morph

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Status: Initialising

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	140.5
Translation (A)	-2.9
Closure (%)	32.7
Bending Residues ( green )	346 - 365
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

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