DNA Polymerase III Alpha Subunit

(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 III Alpha Subunit
  Conformer 1
(PDB)
2hpi (A)
  Conformer 2
(PDB)
3e0d (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 30 0.44   838 - 867
2 804 1.92   7 - 837
3 237 1.24   868 - 1024   1123 - 1203
4 68 0.36   1025 - 1122

Sequence


           ________________________________________________________________________________________________________________________ 
 2hpi(A) : LKFAHLHQHTQFSLLDGAAKLQDLLKWVKETTPEDPALAMTDHGNLFGAVEFYKKATAMGVKPIIGYEAYVAAESRFDRKRgGYFHLTLLAKDFTGYQNLVRLASRAYLEGFYEKPRIDR 
         :                                                                                                                          
 3e0d(A) : LKFAHLHQHTQFSLLNGAAKLQDLLKWVKETTPEDPALAMTDHGNLFGAVEFYKKATAMGVKPIIGYEAYVAAESRFDRKRgGYFHLTLLAKDFTGYQNLVRLASRAYLEGFYEKPRIDR 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2hpi(A) : EILREHAQGLIALSGCLGAEIPQFILQDRLDLAEARLNEDLSIFGDRFFIEIQNHGLPEQKKVNQVLKEFARKYGLGMVATNDGHYVRKEDARAHEVLLAIQSKTTLDDPERWRFPCDEF 
         :                                                                                                                          
 3e0d(A) : EILREHAQGLIALSGCLGAEIPQFILQDRLDLAEARLNEDLSIFGDRFFIEIQNHGLPEQKKVNQVLKEFARKYGLGMVATNNGHYVRKEDARAHEVLLAIQSKTTLDDPERWRFPCDEF 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2hpi(A) : YVKTPEEMRAMLPEAEWGDEPFDNTVEIARMCDVDLPIGDKMVYRIPRFPLgRTEAQYLRELTFLGLLRRYPDRITEAFYREVLRLLdERALAEALARVEEKAWEELRKReWTAEAILHR 
         :                                                                                                                          
 3e0d(A) : YVKTPEEMRAMLPEAEWGDEPFDNTVEIARMCDVDLPIGDKMVYRIPRFPLgRTEAQYLRELTFLGLLRRYPDRITEAFYREVLRLLdERALAEALARVEEKAWEELRKReWTAEAILHR 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2hpi(A) : ALYELSVIERMGFPGYFLIVQDYINWARGHGVSVGPGRGSAAGSLVAYAVGITNIDPLRFGLLFERFLNPERVSMPDIDTDFSDRERDRVIQYVRERYGEDKVAQIGTFGSLASKAALKD 
         :                                                                                                                          
 3e0d(A) : ALYELSVIERMGFPGYFLIVQDYINWARGHGVSVGPGRGSAAGSLVAYAVGITNIDPLRFGLLFERFLNPERVSMPDIDTDFSDRERDRVIQYVRERYGEDKVAQIGTFGSLASKAALKD 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2hpi(A) : VARVYGIPHKKAEELAKLIPVQFGKPKPLQEA-----eLRAEMEKDERIRQVIEVAMRLEGLNRHASVHAAGVVIAAEPLTDLVPLMRDQEGRPVTQYDMGAVEALGLLKMDFLGLRTLT 
         :                                                                                                                          
 3e0d(A) : VARVYGIPHKKAEELAKLIPVQFGKPKPLQEAFEAEPELRAEMEKDERIRQVIEVAMRLEGLNRHASVHaAGVVIAAEPLTDLVPLMRDQEGRPVTQYDMGAVEALGLLKMDFLGLRTLT 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2hpi(A) : FLDEARRIVKESKGVELDYDRLPLDDPKTFELLSRGETKGVFQLESGGMTATVRGLKPRRLEDIIALVSLYRPGPMEHIPTYIRRHHGQEPVSYAEFPHAEKYLRPILDETYGIPVYQEQ 
         :                                                                                                                          
 3e0d(A) : FLDEARRIVKESKGVELDYDRLPLDDPKTFELLSRGETKGVFQLESGGMTATVRGLKPRRLEDIIALVSLYRPGPMEHIPTYIRRHHGQEPVSYAEFPHAEKYLRPILDETYGIPVYQEQ 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________837_______________________863___ 
 2hpi(A) : IMQIASQVAGYSLGEADLLRRAMGKKRVEEMQKHRERFVRGAKERGVPEEEANRLFDMLEAFANYGFNKSHAAAYSLLSYQTAYVKAHYPVEFMAALLSVERHDSDKVAEYIRDARALGI 
         :                                                                                                                          
 3e0d(A) : IMQIASQVAGYSLGEADLLRRAMGKKRVEEMQKHRERFVRGAKERGVPEEEANRLFDMLEAFANYGfNKSHAAAYSLLSYQTAYVKAHYPVEFMAALLSVERHDSDKVAEYIRDARALGI 
           ________________________________________________________________________________________837_______________________863___ 

           ________________________________________________________________________________________________________________________ 
 2hpi(A) : PVLPPDVNRSGFDFKVVGEEILFGLSAVKNVGEMAARAILEERERGGPFKSLGDFLKRLPEQVVNKRALESLVKAGALDAFGDRARLLASLEPLLRWAAETRERGRSGLVGLFAEVEEPP 
         :                                                                                                                          
 3e0d(A) : PVLPPDVNRSGFDFKVVGEEILFGLSAVKNVGEMAARAILEERERGGPFKSLGDFLKRLPEQVVNKRALESLVKAGALDAFGDRARLLASLEPLLRWAAETRERGRSGLVGLFAEVEEPP 
           ________________________________________________________________________________________________________________________ 

           _____________________1011__________________________________________________________________________1119_________________ 
 2hpi(A) : LVEASPLDEITMLRYEKEALGIYVSGHPVLRYPGLREVASCTIEELSEFVRELPGKPKVLLSGMVEEVrFTLSDETGALEVVkEDIPLLVLAEVErVLAQAVWTLEEVLEAPKALEVEVD 
         :                                                                                                                          
 3e0d(A) : LVEASPLDEITMLRYEKEALGIYVSGHPVLRYPGLREVASCTIEELSEFVRELPGKPKVLLSGMVEEVrFTLSDETGALEVVkEDIPLLVLAEVErVLAQAVWTLEEVLEAPKALEVEVD 
           _____________________1011__________________________________________________________________________1119_________________ 

           ____________________________________________________________________                                                     
 2hpi(A) : HALLDEKGaRLKSLLDEHPGSLPVYLRVLGPFGEALFALREVRVGEEALGLLEAEGYRAYLVPDREVF                                                     
         :                                                                                                                          
 3e0d(A) : HALLDEKGaRLKSLLDEHPGSLPVYLRVLGPFGEALFALREVRVGEEALGLLEAEGYRAYLVPDREVF                                                     
           ____________________________________________________________________                                                     

Morph

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Domain Pairs

Fixed Domain Moving Domain Rotation Angle Translation   (A) Closure Bending Residues  
1 2 24.4 0.6 33.9   837 - 838 Bending Region Analysis
1 3 18.3 1.6 50.2   863 - 868 Bending Region Analysis
3 4 24.8 -1.1 54.0   1011 - 1026   1119 - 1131 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

Conformer 1 Contact:
Residue 3 ———› Residue 4

Conformer 2 Contact:
Residue 4 ———› Residue 3

Movement classification: Hinge

PyMOL Script

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