DynDom - Protein Domain Motions

Hiv-1 Reverse Transcriptase

(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	Hiv-1 Reverse Transcriptase
Conformer 1 (PDB)	1vrt (A)
Conformer 2 (PDB)	1ep4 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	130	0.91	231 - 244 313 - 426 511 - 512
2	198	1.26	6 - 214
3	66	0.62	245 - 311
4	98	0.56	427 - 510 513 - 537

Sequence

`________________________________________________________________________________________________________________________` `1vrt(A) : PIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDED` `:` `1ep4(A) : PIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIK------wRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDED` `________________________________________________________________________________________________________________________` `_______________________________________________________________________________________213_________________________241__` `1vrt(A) : FRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQP` `:` `1ep4(A) : FRKYTAFTIPSIN-----iRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPD--hQKEPPFLWMGYELHPDKWTVQP` `_______________________________________________________________________________________213_________________________241__` `_________________________________________________________________311____________________________________________________` `1vrt(A) : IVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTN` `:` `1ep4(A) : IVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQL-kLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTN` `_________________________________________________________________311____________________________________________________` `____________________________________________________________426_________________________________________________________` `1vrt(A) : DVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVD-----------aGYVTNRGRQKVVTLTDTTNQKTELQAIY` `:` `1ep4(A) : DVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIY` `____________________________________________________________426_________________________________________________________` `________________________510_____________________________` `1vrt(A) : LALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAH` `:` `1ep4(A) : LALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAH` `________________________510_____________________________`

Morph

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jsmol/j2s/J/g3d/PixelatorT.js

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JSmol exec jmolApplet start applet null

Jmol JavaScript applet jmolApplet__918193023382726__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet__918193023382726__)

vwrOptions:

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appletId:jmolApplet (signed)

jsmol/j2s/core/corescript.z.js

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Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor #FFFFFF

backgroundColor = "#FFFFFF"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

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Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet__918193023382726__ ready

script 1 started

FileManager.getAtomSetCollectionFromFile(dyndommorphdb/HIVRE1R3.pdb)

FileManager opening 1 https://dyndom.cmp.uea.ac.uk/dyndom/dyndommorphdb/HIVRE1R3.pdb

The Resolver thinks Pdb

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jsmol/j2s/J/shape/Mesh.js

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jsmol/j2s/J/renderbio/RocketRenderer.js

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#jmolScript: select 426- 427, 512- 513

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#jmolScript: select 510- 511

#jmolScript: color [0 ,255,0 ]

#jmolScript: select all

#jmolScript: anim mode loop 0.5 0.5;anim on;

#jmolScript: set echo top left;color echo [x0D0D99];echo "DynDom"

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NUCLEOTIDYLTRANSFERASE 19-APR-95 1VRT

HIGH RESOLUTION STRUCTURES OF HIV-1 RT FROM FOUR RT-

INHIBITOR COMPLEXES

found biomolecule 1: A, B

biomolecule 1: number of transforms: 1

jsmol/j2s/core/coresym.z.js

-- required by ClazzNode ajax=true async=false

Time for openFile(dyndommorphdb/HIVRE1R3.pdb): 2755 ms

reading 104304 atoms

ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false

24 models in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

104304 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

NUCLEOTIDYLTRANSFERASE 19-APR-95 1VRT

HIGH RESOLUTION STRUCTURES OF HIV-1 RT FROM FOUR RT-

INHIBITOR COMPLEXES

found biomolecule 1: A, B

Adding embedded #jmolscript: select ({4201:4345});backbone only;select ({8547:8691});backbone only;select ({12893:13037});backbone only;select ({17239:17383});backbone only;select ({21585:21729});backbone only;select ({25931:26075});backbone only;select ({30277:30421});backbone only;select ({34623:34767});backbone only;select ({38969:39113});backbone only;select ({43315:43459});backbone only;select ({47661:47805});backbone only;select ({52007:52151});backbone only;select ({56353:56497});backbone only;select ({60699:60843});backbone only;select ({65045:65189});backbone only;select ({69391:69535});backbone only;select ({73737:73881});backbone only;select ({78083:78227});backbone only;select ({82429:82573});backbone only;select ({86775:86919});backbone only;select ({91121:91265});backbone only;select ({95467:95611});backbone only;select ({99813:99957});backbone only;select ({104159:104303});backbone only;select *; select all; color grey; background white; select 231- 244, 313- 426, 511- 512; color [0 ,0 ,255]; select 6- 214; color [255,0 ,0 ]; select 540- 581; color [0 ,0 ,255]; backbone 100; select 582- 595; color [255,0 ,0 ]; backbone 100; select 245- 311; color [255,255,0 ]; select 596- 619; color [0 ,0 ,255]; backbone 100; select 620- 633; color [255,255,0 ]; backbone 100; select 427- 510, 513- 537; color [238,130,238]; select 634- 670; color [0 ,0 ,255]; backbone 100; select 671- 684; color [238,130,238]; backbone 100; select 213- 231; color [0 ,255,0 ]; select 241- 246; color [0 ,255,0 ]; select 311- 317; color [0 ,255,0 ]; select 426- 427, 512- 513; color [0 ,255,0 ]; select 510- 511; color [0 ,255,0 ]; select all; anim mode loop 0.5 0.5;anim on; set echo top left;color echo [x0D0D99];echo "DynDom"; set antialiasDisplay ON

24 models

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jsmol/j2s/J/thread/AnimationThread.js

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jsmol/j2s/J/g3d/HermiteRenderer.js

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jsmol/j2s/core/coretext.z.js

-- required by ClazzNode ajax=true async=false

DynDom

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	12.7
Translation (A)	-0.6
Closure (%)	4.5
Bending Residues ( green )	213 - 231
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	14.6
Translation (A)	4.2
Closure (%)	71.2
Bending Residues ( green )	241 - 246 311 - 317
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( violet )	4
Rotation Angle (deg)	13.6
Translation (A)	0.0
Closure (%)	31.1
Bending Residues ( green )	426 - 427 510 - 513
Bending Region Analysis