DynDom - Protein Domain Motions

Transitional Endoplasmic Reticulum Atpase

(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	Transitional Endoplasmic Reticulum Atpase
Conformer 1 (PDB)	1r7r (A)
Conformer 2 (PDB)	1ypw (A)
Window Length	7
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	657	1.81	20 - 484 505 - 732
2	20	3.47	485 - 504

Sequence

`________________________________________________________________________________________________________________________` `1r7r(A) : LKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLK` `:` `1ypw(A) : LKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLK` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1r7r(A) : PYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIAR` `:` `1ypw(A) : PYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIAR` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1r7r(A) : AVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLK--aHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATG` `:` `1ypw(A) : AVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATG` `________________________________________________________________________________________________________________________` `___________________________________________________________________________________________________478__________________` `1r7r(A) : RLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYP` `:` `1ypw(A) : RLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYP` `___________________________________________________________________________________________________478__________________` `__501___________________________________________________________________________________________________________________` `1r7r(A) : VEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDnVFIIGA` `:` `1ypw(A) : VEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDnVFIIGA` `__501___________________________________________________________________________________________________________________` `____________________________________________________________________________________________` `1r7r(A) : TNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSdVDLEFLAKMTNGFSGADLTEICQRACKLAIRESpVPEIRRDH*******` `:` `1ypw(A) : TNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSdVDLEFLAKMTNGFSGADLTEICQRACKLAIRESpVPEIRRDHFEEAMRF` `____________________________________________________________________________________________`

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)	95.9
Translation (A)	-4.9
Closure (%)	94.7
Bending Residues ( green )	478 - 485 501 - 505
Bending Region Analysis

Dynamic Contact Graph

The dynamic contact graph is still being generated. Progress: Initialising

PyMOL Script

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