DNA Helicase II

(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 Helicase II
  Conformer 1
(PDB)
2is6 (A)
  Conformer 2
(PDB)
3lfu (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 213 1.1   29 - 34   223 - 225   248 - 260   281 - 306   310 - 379   549 - 645
2 253 1.93   5 - 28   35 - 222   226 - 247   261 - 280   307 - 309
3 155 1.31   380 - 539

Sequence


           __________________________28____34______________________________________________________________________________________ 
 2is6(A) : MDVSYLLDSLNDKQREAVAAPRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLMGTSQGGMWVGTFHGLAHRLLRAHHMDANLPQDFQILDSEDQL 
         :                                                                                                                          
 3lfu(A) : **VSYLLDSLNDKQREAVAAPRSNLLVLAGAGSGKTRVLVHRIAWLMSVENCSPYSIMAVTFTNKAAAEMRHRIGQLMGTSQGGMWVGTFHGLAHRLLRAHHMDANLPQDFQILDSEDQL 
           __________________________28____34______________________________________________________________________________________ 

           ___________________________________________________________________________________________________222__________________ 
 2is6(A) : RLLKRLIKAMNLDEKQWPPRQAMWYINSQKDEGLRPHHIQSYGNPVEQTWQKVYQAYQEACDRAGLVDFAELLLRAHELWLNKPHILQHYRERFTNILVDEFQDTNNIQYAWIRLLAGDT 
         :                                                                                                                          
 3lfu(A) : RLLKRLIKAMNLDEKQWPPRQAMWYINSQKDEGLRPHHI----nPVEQTWQKVYQAYQEACDRAGLVDFAELLLRAHELWLNKPHILQHYRERFTNILVDEFQDTNNIQYAWIRLLAGDT 
           ___________________________________________________________________________________________________222__________________ 

           ____247__________260_________________280____________________303___309___________________________________________________ 
 2is6(A) : GKVMIVGDDDQSIYGWRGAQVENIQRFLNDFPGAETIRLEQNYRSTSNILSAANALIENNNGRLGKKLWTDGADGEPISLYCAFNELDEARFVVNRIKTWQDNGGALAECAILYRSNAQS 
         :                                                                                                                          
 3lfu(A) : GKVMIVGDDDQSIYGWRGAQVENIQRFLNDFPGAETIRLEQNYRSTSNILSAANALIENNNGRLGKKLWTDGADGEPISLYCAFNELDEARFVVNRIKTWQDNGGALAECAILYRSNAQS 
           ____247__________260_________________280____________________303___309___________________________________________________ 

           ____________375_________________________________________________________________________________________________________ 
 2is6(A) : RVLEEALLQASMPYRIYGGMRFFERQEIKDALSYLRLIVNRNDDAAFERVVNTPTRGIGDRTLDVVRQTSRDRQLTLWQACRELLQEKALAGRAASALQRFMELIDALAQETADMPLHVQ 
         :                                                                                                                          
 3lfu(A) : RVLEEALLQASMPYRIYGGMRFFERQEIKDALSYLRLIANRNDDAAFERVVNTPTRGIGDRTLDVVRQTSRDRQLTLWQACRELLQEKALAGRAASALQRFMELIDALAQETADMPLHVQ 
           ____________375_________________________________________________________________________________________________________ 

           ______________________________________________________539_______________________________________________________________ 
 2is6(A) : TDRVIKDSGLRTMYEQEKGEKGQTRIENLEELVTATRQFSYNEeDLMPLQAFLSHAALEAGEGQADTWQDAVQLMTLHSAKGLEFPQVFIVGMEEGMFPSQMSLDEGGRLEEERRLAYVG 
         :                                                                                                                          
 3lfu(A) : TDRVIKDSGLRTMYEQEKGEKGQTRIENLEELVTATRQFS---eDLMPLQAFLSHAALE-gEGQADTWQDAVQLMTLHSAKGLEFPQVFIVGMEEGMFPSQMSL--gGRLEEERRLAYVG 
           ______________________________________________________539_______________________________________________________________ 

           ______________________________________________________                                                                   
 2is6(A) : VTRAMQKLTLTYAETRRLYGKEVYHRPSRFIGELPEECVEEVRLRATVSRPVSH                                                                   
         :                                                                                                                          
 3lfu(A) : VTRAMQKLTLTYAETRRLYGKEVYHRPSRFIGELPEECVEEVRLR*********                                                                   
           ______________________________________________________                                                                   

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
29.0
Translation
(A)
0.5
Closure
(%)
75.1
Bending Residues
( green )
  28 - 30
  34 - 35
  222 - 223
  225 - 226
  247 - 248
  260 - 261
  280 - 281
  303 - 307
  309 - 310
Bending Region Analysis
Property Value
Fixed Domain
( blue )
1
Moving Domain
( yellow )
3
Rotation Angle
(deg)
142.6
Translation
(A)
3.4
Closure
(%)
17.6
Bending Residues
( green )
  375 - 381
  539 - 553
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

Conformer 1 Contact:
Residue 1 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 1

Movement classification: Hinge

PyMOL Script

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