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

PyMOL Script

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