DNA Ligase

(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 Ligase
  Conformer 1
(PDB)
1dgs (A)
  Conformer 2
(PDB)
1dgs (B)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 343 0.66   4 - 269   277 - 282   284 - 312   321 - 332   336 - 336   339 - 343   353 - 356   363 - 363   366 - 367   375 - 384   408 - 408   414 - 419
2 232 0.8   270 - 276   283 - 283   313 - 320   333 - 335   337 - 338   344 - 352   357 - 362   364 - 365   368 - 374   385 - 407   409 - 413   420 - 578

Sequence


           ________________________________________________________________________________________________________________________ 
 1dgs(A) : MTREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGARPLEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERLEREAEAPSLYTVEHKVDGL 
         :                                                                                                                          
 1dgs(B) : MTREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGARPLEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERLEREAEAPSLYTVEHKVDGL 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1dgs(A) : SVLYYEEGVWSTGSGDGEVGEEVTQNLLTIPTIPRRLKGVPDRLEVRGEVYMPIEAFLRLNEELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLGLEESGLKSQYEL 
         :                                                                                                                          
 1dgs(B) : SVLYYEEGVWSTGSGDGEVGEEVTQNLLTIPTIPRRLKGVPDRLEVRGEVYMPIEAFLRLNEELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLGLEESGLKSQYEL 
           ________________________________________________________________________________________________________________________ 

           __________________________269____276___282___________________________312_____320_________332________343______352_356___3 
 1dgs(A) : LLWLKEKGFPVEHCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKLDDLTLWGELGYTARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHNES 
         :                                                                                                                          
 1dgs(B) : LLWLKEKGFPVEHCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKLDDLTLWGELGYTARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHNES 
           _________________________2269___2276__2282__________________________2312____2320________2332_______2343_____2352______23 

           62_________374_______384____________________407___413___419_____________________________________________________________ 
 1dgs(A) : YIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGKERPIRWPEACPECGHRLVKEGKVHRCPNPLCPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRKEDLLGL 
         :                                                                                                                          
 1dgs(B) : YIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGKERPIRWPEACPECGHRLVKEGKVHRCPNPLCPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRKEDLLGL 
           62________2374______2384___________________2407__2413__2419_____________________________________________________________ 

           _____________________________________________________________________________________________________                    
 1dgs(A) : ERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEASLEELIEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVSMESK                    
         :                                                                                                                          
 1dgs(B) : ERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEASLEELIEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVSMESK                    
           _____________________________________________________________________________________________________                    

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
3.1
Translation
(A)
-0.2
Closure
(%)
46.3
Bending Residues
( green )
  269 - 270
  276 - 277
  282 - 284
  312 - 318
  320 - 321
  332 - 333
  335 - 339
  343 - 344
  352 - 353
  356 - 357
  362 - 368
  374 - 375
  384 - 385
  407 - 409
  413 - 414
  419 - 420
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

PyMOL Script

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