DynDom - Protein Domain Motions

Rna-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	Rna-Directed RNA Polymerase
Conformer 1 (PDB)	2xxd (A)
Conformer 2 (PDB)	4e78 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	287	0.91	6 - 11 14 - 19 44 - 139 157 - 190 198 - 211 216 - 216 218 - 313 322 - 325 327 - 350 363 - 368
2	242	1.88	12 - 13 20 - 43 140 - 156 191 - 197 212 - 215 217 - 217 314 - 321 326 - 326 351 - 362 369 - 542

Sequence

`__________11______________________________43____________________________________________________________________________` `2xxd(A) : SMSYSWTGALITPCSPEEEKLPINPLSNSLLRYHNKVYCTTSKSASQRAKKVTFDRTQVLDAHYDSVLKDIKLAASKVSARLLTLEEACQLTPPHSARSKYGFGAKEVRSLSGRAVNHI` `:` `4e78(A) : SSMSYSWTGALITPCSPEEEKLPINPLSNSLLRYHNKVYCTTSKSASQRAKKVTFDRTQVLDAHYDSVLKDIKLAASKVSARLLTLQQACQLTPPHSARSKYGFGAKEVRSLSGRAVNHI` `__________11______________________________43____________________________________________________________________________` `_________________139______________156_______________________________190____197___________211_215________________________` `2xxd(A) : KSVWKDLLEDPQTPIPTTIMAKNEVFCVDPAKGGKKPARLIVYPDLGVRVCEKMALYDITQKLPQAVMGASYGFQYSPAQRVEYLLKAWAEKKDPMGFSYDTRCFDSTVTERDIRTEESI` `:` `4e78(A) : KSVWKDLLEDPQTPIPTTIMAKNEVFCVDPAKGGKKPARLIVYPDLGVRVCEKMALYDITQKLPQAVMGASYGFQYSPAQRVEYLLKAWAEKKDPMGFSYDTRCFDSTVTERDIRTEESI` `_________________139______________156_______________________________190____197___________211_215________________________` `_______________________________________________________________________313_____321_325______________________350_________` `2xxd(A) : YQACSLPEEARTAIHSLTERLYVGGPMFNSKGQTCGYRRCRASGVLTTSMGNTITCYVKALAACKAAGIVAPTMLVCGDDLVVISESQGTEEDERNLRAFTEAMTRYSAPPGDPPRPEYD` `:` `4e78(A) : YQACSLPEEARTAIHSLTERLYVGGPMFNSKGQTCGYRRCRASGVLTTSMGNTITCYVKALAACKAAGIVAPTMLVCGDDLVVISESQGTEEDERNLRAFTEAMTRYSAPPGDPPRPEYD` `_______________________________________________________________________313_____321_325______________________350_________` `362_366_________________________________________________________________________________________________________________` `2xxd(A) : LELITSCSSNVSVALGPRGRRRYYLTRDPTTPLARAAWETVRHSPINSWLGNIIQYAPTIWVRMVLMTHFFSILMVQDTLDQNLNFEMYGSVYSVNPLDLPAIIERLHGLDAFSMHTYSH` `:` `4e78(A) : LELITSCSSNVSVALGPRGRRRYYLTRDPTTPLARAAWETVRHSPINSWLGNIIQYAPTIWVRMVLMTHFFSILMVQDTLDQNLG--------GVNPLDLPAIIERLHGLDAFSMHTYSH` `362_366_________________________________________________________________________________________________________________` `____________________________________________________________________________________` `2xxd(A) : HELTRVASALRKLGAPPLRVWKSRARAVRASLISRGGKAAVCGRYLFNWAVKTKLKLTPLPEARLLDLSSWFTVGAGGGDIFHS` `:` `4e78(A) : HELTRVASALRKLGAPPLRVWKSRARAVRASLISRGGKAAVCGRYLFNWAVKTKLKLTPLPEARLL*****************` `____________________________________________________________________________________`

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)	12.0
Translation (A)	0.2
Closure (%)	100.0
Bending Residues ( green )	11 - 25 43 - 44 139 - 140 156 - 157 190 - 191 197 - 198 211 - 212 215 - 218 313 - 314 321 - 322 325 - 327 350 - 351 362 - 363 366 - 369
Bending Region Analysis

Dynamic Contact Graph

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

PyMOL Script

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