DynDom - Protein Domain Motions

T7 RNA Polymerase

(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	T7 RNA Polymerase
Conformer 1 (PDB)	1aro (P)
Conformer 2 (PDB)	2pi4 (A)
Window Length	11
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	523	2.05	36 - 540 724 - 725 731 - 732 736 - 813 816 - 823 841 - 842 844 - 845
2	218	2.12	541 - 723 726 - 730 733 - 735 814 - 815 824 - 840 843 - 843 846 - 874

Sequence

`________________________________________________________________________________________________________________________` `1aro(P) : KNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLliTTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASA` `:` `2pi4(A) : *********************IAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFpLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYIT` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1aro(P) : IGRAIEDEARFGRIRDLEAKHFKKfMQVVEADMLSKGLLGGEAWSS-----------------WHKEDSIHVGVRCIEMLIESTGMVSLHRQNsETIELAPEYAEAIATRAGALA-----` `:` `2pi4(A) : IKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVG` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1aro(P) :` `--GISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWvYRKDKARKSRRISLEFMLEQA--------------` `:` `2pi4(A) :` `QDSETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIERE` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1aro(P) :` `-------------------------NKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENT` `:` `2pi4(A) :` `ELPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPER` `________________________________________________________________________________________________________________________` `_____________________________________540________________________________________________________________________________` `1aro(P) : WWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGgTKALAGQWLAYGVTRSVTKRS---------` `:` `2pi4(A) : IKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVT` `_____________________________________518________________________________________________________________________________` `____________________________________________________________________________________________________723____730__735_____` `1aro(P) :` `-------------VMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRSAVHWVTPDGFPVWQEYK` `:` `2pi4(A) :` `DENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEI` `____________________________________________________________________________________________________701____708__713_____` `______________________________________________________________________813_______823______________840____________________` `1aro(P) : KPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESSDVLADFYDQFADQLHESQLDK` `:` `2pi4(A) : LRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYES` `______________________________________________________________________791_______801______________818____________________` `_____________________________________________` `1aro(P) : MPALPAKGNLNLRDILESD************************` `:` `2pi4(A) : CDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA` `_____________________________________________`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	9.9
Translation (A)	-0.1
Closure (%)	98.3
Bending Residues ( green )	540 - 541 723 - 726 730 - 733 735 - 736 813 - 816 823 - 824 840 - 846
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

PyMOL Script

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