DynDom - Protein Domain Motions

Dna-Directed 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	Dna-Directed RNA Polymerase
Conformer 1 (PDB)	1s0v (A)
Conformer 2 (PDB)	1cez (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	640	5.15	17 - 73 258 - 881
2	149	2.59	74 - 164 200 - 257

Sequence

`__________________________________________45____________________________________________________________________________` `1s0v(A) : NTINIAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKT` `:` `1cez(A) : ****IAKNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMF----------------pLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKT` `__________________________________________45____________________________________________________________________________` `________________________________________________________________________________________________________________________` `1s0v(A) : TLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDS` `:` `1cez(A) : TLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDS` `________________________________________________________________________________________________________________________` `____________256_________________________________________________________________________________________________________` `1s0v(A) : ETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIe-----` `:` `1cez(A) : ETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELP` `____________256_________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1s0v(A) :` `-----------ALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKF` `:` `1cez(A) :` `MKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKF` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1s0v(A) : IEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDEN` `:` `1cez(A) : IEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDEN` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1s0v(A) : TGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRK` `:` `1cez(A) : TGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRK` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1s0v(A) : RCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFR---------dSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDV` `:` `1cez(A) : RCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDV` `________________________________________________________________________________________________________________________` `__________________________________________` `1s0v(A) : LADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA` `:` `1cez(A) : LADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESDFAFA` `__________________________________________`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
For more advanced options, right click on the model.

play backwards

pause

play forwards

Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	133.0
Translation (A)	-23.8
Closure (%)	12.9
Bending Residues ( green )	45 - 74 256 - 268
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

PyMOL Script

Download and extract PyMOL PML script file

Download