DynDom - Protein Domain Motions

Pneumolysin

(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	Pneumolysin
Conformer 1 (PDB)	5cr6 (D)
Conformer 2 (PDB)	5ly6 (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	34	10.02	27 - 37 42 - 42 51 - 53 341 - 359
2	253	5.47	3 - 26 54 - 157 185 - 254 282 - 340
3	122	6.23	38 - 41 43 - 50 360 - 469

Sequence

`_______________________25__________37_____________52____________________________________________________________________` `5cr6(D) : MANKAVNDFILAMNYDKKKLLTHQGESIENRFIKEGNQLPDEFVVIERKKRSLSTNTSDISVTATNDSRLYPGALLVVDETLLENNPTLLAVDRAPMTYSIDLPGLASSDSFLQVEDPSN` `:` `5ly6(B) : MANKAVNDFILAMNYDKKKLLTHQGESIENRFIKEGNQLPDEFVVIERKKRSLSTNTSDISVTATNDSRLYPGALLVVDETLLENNPTLLAVDRAPMTYSIDLPGLASSDSFLQVEDPSN` `_______________________25__________37_____________52____________________________________________________________________` `________________________________________________________________________________________________________________________` `5cr6(D) : SSVRGAVNDLLAKWHQDYGQVNNVPARMQYEKITAHSMEQLKVKFGSDFEKTGNSLDIDFNSVHSGEKQIQIVNFKQIYYTVSVDAVKNPGDVFQDTVTVEDLKQRGISAERPLVYISSV` `:` `5ly6(B) : SSVRGAVNDLLAKWHQDYGQVNNVPARMQYEKITAHSMEQLKVKFGSDFEKAANSLDIDFNAVHSGEKQIQIVNFKQIYYTVSVDAVKNPGDVFQDTVTVEDLKQRGISAERPLVYISSV` `________________________________________________________________________________________________________________________` `_________________________________________________________________________________________________340________________359_` `5cr6(D) : AYGRQVYLKLETTSKSDEVEAAFEALIKGVKVAPQTEWKQILDNTEVKAVILG----sGARVVTGKVDMVEDLIQEGSRFTADHPGLPISYTTSFLRDNVVATFQNSTDYVETKVTAYRN` `:` `5ly6(B) : AYGRQVYLKLETTSKSDEVQAAFEAAILGVKVAPQTQWKQILDNTEVKAVILGGDPSSGARVVTGKVDMVEDLIQEGSRFTADHPGLPISYTTSFLRDNVVATFQNSTDYVETKVTAYRN` `_________________________________________________________________________________________________340________________359_` `_______________________________________________________________________________________________________________` `5cr6(D) : GDLLLDHSGAYVAQYYITWDELSYNHQGKEVLTPKAWDRNGQDLTAHFTTSIPLKGNVRNLSVKIREATGLAWEWWRTVYEKTDLPLVRKRTISIWGTTLYPQVEDKVEND` `:` `5ly6(B) : GDLLLDHSGAYVAQYYITWDELSYDHQGKEVLTPKAWDRNGQDLTAHFTTSIPLKGNVRNLSVKIRECTGLAWEWWRTVYEKTDLPLVRKRTISIWGTTLYPQVEDKVEND` `_______________________________________________________________________________________________________________`

Morph

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Status: Initialising

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)	89.7
Translation (A)	8.2
Closure (%)	20.9
Bending Residues ( green )	25 - 27 52 - 56 340 - 341
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	81.7
Translation (A)	3.7
Closure (%)	84.6
Bending Residues ( green )	37 - 51 359 - 361
Bending Region Analysis