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

Domains

Domain Size Backbone RMSD
(A)
Residues
1 787 1.57   4 - 484   559 - 890
2 71 1.66   485 - 558

Sequence


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

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

           ________________________________________________________________________________________________________________________ 
 2dy4(C) : RLSPHRKTRVKVIENyGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLD-gYYAKIQIQSVFSP 
         :                                                                                                                          
 2dtu(A) : RLSPHRKTRVKV----G--EIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFSP 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2dy4(C) : IKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYV-sFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNG--yYKDRDGVVPTEITKVFNQ 
         :                                                                                                                          
 2dtu(A) : IKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQ 
           ________________________________________________________________________________________________________________________ 

           484_______________________________________________________________________558___________________________________________ 
 2dy4(C) : RKEHKGY-lAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNE-lFRAQRTEVAG-tAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQ-aLQWIERKV 
         :                                                                                                                          
 2dtu(A) : RKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKV 
           484_______________________________________________________________________558___________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2dy4(C) : NEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARER-ePAIDRGFRE-cEY-nNKQHLf--dREAIAGPPLGSKGIGGFWTGKKRYALNVWD-eGTRYA 
         :                                                                                                                          
 2dtu(A) : NEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRYA 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2dy4(C) : EPKLKI-gLETQKSSTPKAVQKALKECIRR-lQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPF 
         :                                                                                                                          
 2dtu(A) : EPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPF 
           ________________________________________________________________________________________________________________________ 

           ______________________________________________________________                                                           
 2dy4(C) : GDKCIAWPSGTEITDLIKDDVLHW-dYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFD****                                                           
         :                                                                                                                          
 2dtu(A) : GDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFDF                                                           
           ______________________________________________________________                                                           

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
12.5
Translation
(A)
1.5
Closure
(%)
35.6
Bending Residues
( green )
  484 - 485
  558 - 559
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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