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)
1ig9 (A)
  Conformer 2
(PDB)
2dy4 (C)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 791 1.59   4 - 479   481 - 481   564 - 897
2 80 1.72   480 - 480   482 - 563

Sequence


           ________________________________________________________________________________________________________________________ 
 1ig9(A) : MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSP 
         :                                                                                                                          
 2dy4(C) : *KEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFAN-rDASQWIKR-eDIGLEALG-dDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSP 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1ig9(A) : DGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAK 
         :                                                                                                                          
 2dy4(C) : DGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIY-pFDNEKELL-eYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAK 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1ig9(A) : RLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFS 
         :                                                                                                                          
 2dy4(C) : RLSPHRKTRVKVIEN-yGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLD-gYYAKIQIQSVFS 
           ________________________________________________________________________________________________________________________ 

           _______________________________________________________________________________________________________________474______ 
 1ig9(A) : PIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFN 
         :                                                                                                                          
 2dy4(C) : PIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYV-sFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNG--yYKDRDGVVPTEITKVFN 
           _______________________________________________________________________________________________________________474______ 

           ________________________________________________________________________________563_____________________________________ 
 1ig9(A) : QRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERK 
         :                                                                                                                          
 2dy4(C) : QRKEHKGY-lAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNE-lFRAQRTEVAG-tAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQ-aLQWIERK 
           ________________________________________________________________________________563_____________________________________ 

           ________________________________________________________________________________________________________________________ 
 1ig9(A) : VNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRY 
         :                                                                                                                          
 2dy4(C) : VNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARER-ePAIDRGFRE-cEY-nNKQHLf--dREAIAGPPLGSKGIGGFWTGKKRYALNVWD-eGTRY 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1ig9(A) : AEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNP 
         :                                                                                                                          
 2dy4(C) : AEPKLKI-gLETQKSSTPKAVQKALKECIRR-lQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNP 
           ________________________________________________________________________________________________________________________ 

           _____________________________________________________________                                                            
 1ig9(A) : FGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMF                                                            
         :                                                                                                                          
 2dy4(C) : FGDKCIAWPSGTEITDLIKDDVLHW-dYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFD**                                                            
           _____________________________________________________________                                                            

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)
43.6
Translation
(A)
-2.0
Closure
(%)
49.0
Bending Residues
( green )
  474 - 482
  563 - 568
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

PyMOL Script

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