DynDom - Protein Domain Motions

Property	Value
Name	Aspartate Aminotransferase
Conformer 1 (PDB)	1asn (A)
Conformer 2 (PDB)	1asm (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domain	Size	Backbone RMSD (A)	Residues
1	290	0.3	40 - 333 357 - 360
2	92	0.59	17 - 39 334 - 356 361 - 407

Sequence

`_______________________________37_______________________________________________________________________________________` `1asn(A) : MFENITAAPADPILGLADLFRADERPGKINLGIGVYKDETGKTPVLTSVKKAEQYLLENETTKNYLGIDGIPEFGRCTQELLFGKGSALINDKRARTAQTPGGTGALRVAADFLAKNTSV` `:` `1asm(A) : MFENITAAPADPILGLADLFRADERPGKINLGIGVYKDETGKTPVLTSVKKAEQYLLENETTKNYLGIDGIPEFGRCTQELLFGKGSALINDKRARTAQTPGGTGALRVAADFLAKNTSV` `_______________________________37_______________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1asn(A) : KRVWVSNPSWPNHKSVFNSAGLEVREYAYYDAENHTLDFDALINSLNEAQAGDVVLFHGCCHNPTGIDPTLEQWQTLAQLSVEKGWLPLFDFAYQGFARGLEEDAEGLRAFAAMHKELIV` `:` `1asm(A) : KRVWVSNPSWPNHKSVFNSAGLEVREYAYYDAENHTLDFDALINSLNEAQAGDVVLFHGCCHNPTGIDPTLEQWQTLAQLSVEKGWLPLFDFAYQGFARGLEEDAEGLRAFAAMHKELIV` `________________________________________________________________________________________________________________________` `______________________________________________________________________________333____________________356_360____________` `1asn(A) : ASSYSKNFGLYNERVGACTLVAADSETVDRAFSQMKAAIRANYSNPPAHGASVVATILSNDALRAIWEQELTDMRQRIQRMRQLFVNTLQEKGANRDFSFIIKQNGMFSFSGLTKEQVLR` `:` `1asm(A) : ASSYSKNFGLYNERVGACTLVAADSETVDRAFSQMKAAIRANYSNPPAHGASVVATILSNDALRAIWEQELTDMRQRIQRMRQLFVNTLQEKGANRDFSFIIKQNGMFSFSGLTKEQVLR` `______________________________________________________________________________333____________________356_360____________` `____________________________________` `1asn(A) : LREEFGVYAVASGRVNVAGMTPDNMAPLCEAIVAVL` `:` `1asm(A) : LREEFGVYAVASGRVNVAGMTPDNMAPLCEAIVAVL` `____________________________________`

Morph

jsmol/j2s/core/package.js

-- required by ClazzNode ajax=false async=true

jsmol/j2s/core/core.z.js

-- required by ClazzNode ajax=false async=true

jsmol/j2s/J/g3d/PixelatorT.js

-- required by J.g3d.Graphics3D ajax=false async=true

JSmol exec jmolApplet start applet null

Jmol JavaScript applet jmolApplet__751843280069371__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet__751843280069371__)

vwrOptions:

{ "name":"jmolApplet","applet":true,"documentBase":"https://dyndom.cmp.uea.ac.uk/dyndom/dyndomRun.do;jsessionid=8f9507572ecb8073f63a60476717?ddid=ASPAR4R17&action=view","platform":"J.awtjs2d.Platform","fullName":"jmolApplet__751843280069371__","codePath":"https://dyndom.cmp.uea.ac.uk/dyndom/jsmol/j2s/","display":"jmolApplet_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"751843280069371","bgcolor":"#FFFFFF" }

setting document base to "https://dyndom.cmp.uea.ac.uk/dyndom/dyndomRun.do;jsessionid=8f9507572ecb8073f63a60476717?ddid=ASPAR4R17&action=view"

Jmol Version: 14.2.12_2015.02.11 2015-02-11 06:00

java.vendor: Java2Script (HTML5)

java.version: 2014-12-19 08:17:57 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet (signed)

jsmol/j2s/core/corescript.z.js

-- required by ClazzNode ajax=true async=false

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

language=en_US

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet__751843280069371__ ready

script 1 started

FileManager.getAtomSetCollectionFromFile(dyndommorphdb/ASPAR4R17.pdb)

FileManager opening 1 https://dyndom.cmp.uea.ac.uk/dyndom/dyndommorphdb/ASPAR4R17.pdb

The Resolver thinks Pdb

jsmol/j2s/core/corebio.z.js

-- required by ClazzNode ajax=true async=false

jsmol/j2s/J/render/MeshRenderer.js

-- required by J.renderbio.BioShapeRenderer ajax=true async=false

jsmol/j2s/J/shape/Mesh.js

-- required by J.renderbio.BioShapeRenderer ajax=true async=false

jsmol/j2s/J/renderbio/RocketRenderer.js

-- required by J.renderbio.RocketsRenderer ajax=true async=false

#jmolScript: select all; color grey; background white;

#jmolScript: select 40- 333, 357- 360

#jmolScript: color [0 ,0 ,255]

#jmolScript: select 17- 39, 334- 356, 361- 407

#jmolScript: color [255,0 ,0 ]

#jmolScript: select 410- 430

#jmolScript: color [0 ,0 ,255]

#jmolScript: backbone 100;

#jmolScript: select 431- 444

#jmolScript: color [255,0 ,0 ]

#jmolScript: backbone 100;

#jmolScript: select 333- 334, 360- 363

#jmolScript: color [0 ,255,0 ]

#jmolScript: select 37- 40, 356- 357

#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"

#jmolScript: set antialiasDisplay ON

AMINOTRANSFERASE 16-SEP-93 1ASN

CRYSTAL STRUCTURES OF ESCHERICHIA COLI ASPARTATE AMINOTRANSF

TWO CONFORMATIONS: COMPARISON OF AN UNLIGANDED OPEN AND TWO

CLOSED FORMS

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/ASPAR4R17.pdb): 3159 ms

reading 74496 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

74496 atoms created

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

AMINOTRANSFERASE 16-SEP-93 1ASN

CRYSTAL STRUCTURES OF ESCHERICHIA COLI ASPARTATE AMINOTRANSF

TWO CONFORMATIONS: COMPARISON OF AN UNLIGANDED OPEN AND TWO

CLOSED FORMS

found biomolecule 1: A, B

Adding embedded #jmolscript: select ({3069:3103});backbone only;select ({6173:6207});backbone only;select ({9277:9311});backbone only;select ({12381:12415});backbone only;select ({15485:15519});backbone only;select ({18589:18623});backbone only;select ({21693:21727});backbone only;select ({24797:24831});backbone only;select ({27901:27935});backbone only;select ({31005:31039});backbone only;select ({34109:34143});backbone only;select ({37213:37247});backbone only;select ({40317:40351});backbone only;select ({43421:43455});backbone only;select ({46525:46559});backbone only;select ({49629:49663});backbone only;select ({52733:52767});backbone only;select ({55837:55871});backbone only;select ({58941:58975});backbone only;select ({62045:62079});backbone only;select ({65149:65183});backbone only;select ({68253:68287});backbone only;select ({71357:71391});backbone only;select ({74461:74495});backbone only;select *; select all; color grey; background white; select 40- 333, 357- 360; color [0 ,0 ,255]; select 17- 39, 334- 356, 361- 407; color [255,0 ,0 ]; select 410- 430; color [0 ,0 ,255]; backbone 100; select 431- 444; color [255,0 ,0 ]; backbone 100; select 333- 334, 360- 363; color [0 ,255,0 ]; select 37- 40, 356- 357; 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

jsmol/j2s/core/corescriptmath.z.js

-- required by ClazzNode ajax=true async=false

jsmol/j2s/J/thread/AnimationThread.js

-- required by ClazzNode ajax=true async=false

jsmol/j2s/J/g3d/HermiteRenderer.js

-- required by ClazzNode ajax=true async=false

jsmol/j2s/core/coretext.z.js

-- required by ClazzNode ajax=true async=false

DynDom

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

Show console

play backwards

pause

play forwards

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	7.1
Translation (A)	-0.1
Closure (%)	98.9
Bending Residues ( green )	37 - 40 333 - 334 356 - 357 360 - 363
Bending Region Analysis

Aspartate Aminotransferase

DynDom run details

Domains

Sequence

Morph

Domain Pairs

Dynamic Contact Graph

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

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

Movement classification: Hinge

PyMOL Script

Aspartate Aminotransferase

DynDom run details

Domains

Sequence

Morph

Domain Pairs

Dynamic Contact Graph

Full-size image

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

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

Movement classification: Hinge

PyMOL Script

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

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