DynDom - Protein Domain Motions

DNA 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 Polymerase
Conformer 1 (PDB)	1rv2 (D)
Conformer 2 (PDB)	1clq (A)
Window Length	7
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	686	1.18	7 - 488 554 - 731 740 - 766 869 - 893
2	103	1.61	732 - 739 767 - 868

Sequence

`________________________________________________________________________________________________________________________` `1rv2(D) : KEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFAN-rDASQWIKR-eDIGLEALG-dDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSP` `:` `1clq(A) : MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSP` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1rv2(D) : DGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIY-pFDNEKELL-eYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAK` `:` `1clq(A) : DGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFDIPYVYNRIKNIFGESTAK` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1rv2(D) : RLSPHRKTRVKV--------eIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLD-gYYAKIQIQSVFS` `:` `1clq(A) : RLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIDVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFS` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1rv2(D) : PIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYV-sFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNG--yYKDRDGVVPTEITKVFN` `:` `1clq(A) : PIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFN` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1rv2(D) : QRKEHKGY-lAAQRNGEIIKEA----------------------------------sLNE-lFRAQRTEVAG-tAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQ-aLQWIERK` `:` `1clq(A) : QRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERK` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1rv2(D) : VNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARER-ePAIDRGFRE-cEY-nNKQHLf--dREAIAGPPLGSKGIGGFWTGKKRYALNVWD-eGTRY` `:` `1clq(A) : VNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRY` `________________________________________________________________________________________________________________________` `________731_____739________________________766__________________________________________________________________________` `1rv2(D) : AEPKLKI-gLETQKSSTPKAVQKALKECIRR-lQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAI------pQVVEGEKVYVLPLREGNP` `:` `1clq(A) : AEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNP` `________731_____739________________________766__________________________________________________________________________` `_________________________868___________________________________` `1rv2(D) : FGDKCIAWPSGTEITDLIKDDVLHW-dYTVLLEKTFIKPLEGFTSAAKLDYEKKAS******` `:` `1clq(A) : FGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFDF` `_________________________868___________________________________`

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)	9.5
Translation (A)	-1.4
Closure (%)	97.9
Bending Residues ( green )	731 - 732 739 - 740 766 - 767 868 - 869
Bending Region Analysis

Dynamic Contact Graph

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

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