Bacterial Sialidase

(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 Bacterial Sialidase
  Conformer 1
(PDB)
2bzd (A)
  Conformer 2
(PDB)
2bzd (C)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 71 0.46   402 - 414   424 - 448   458 - 468   479 - 491   493 - 501
2 353 0.38   50 - 401   492 - 492
3 172 0.49   415 - 423   449 - 457   469 - 478   502 - 645

Sequence


           ________________________________________________________________________________________________________________________ 
 2bzd(A) : GEPLYTEQDLAVNGREGFPNYRIPALTVTPDGDLLASYDGRPTGIDAPGPNSILQRRSTDGGRTWGEQQVVSAGQTTAPIKGFSDPSYLVDRETGTIFNFHVYSQRQGFAGSRPGTDPAD 
         :                                                                                                                          
 2bzd(C) : *EPLYTEQDLAVNGREGFPNYRIPALTVTPDGDLLASYDGRPTGIDAPGPNSILQRRSTDGGRTWGEQQVVSAGQTTAPIKGFSDPSYLVDRETGTIFNFHVYSQRQGFAGSRPGTDPAD 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 2bzd(A) : PNVLHANVATSTDGGLTWSHRTITADITPDPGWRSRFAASGEGIQLRYGPHAGRLIQQYTIINAAGAFQAVSVYSDDHGRTWRAGEAVGVGMDANKTVELSDGRVLLNSRDSARSGYRKV 
         :                                                                                                                          
 2bzd(C) : PNVLHANVATSTDGGLTWSHRTITADITPDPGWRSRFAASGEGIQLRYGPHAGRLIQQYTIINAAGAFQAVSVYSDDHGRTWRAGEAVGVGMDANKTVELSDGRVLLNSRDSARSGYRKV 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________401_____ 
 2bzd(A) : AVSTDGGHSYGPVTIDRDLPDPTNNASIIRAFPDAPAGSARAKVLLFSNAASQTSRSQGTIRMSCDDGQTWPVSKVFQPGSMSYSTLTALPDGTYGLLYEPGTGIRYANFNLAWLGGICA 
         :                                                                                                                          
 2bzd(C) : AVSTDGGHSYGPVTIDRDLPDPTNNASIIRAFPDAPAGSARAKVLLFSNAASQTSRSQGTIRMSCDDGQTWPVSKVFQPGSMSYSTLTALPDGTYGLLYEPGTGIRYANFNLAWLGGICA 
           ________________________________________________________________________________________________________________401_____ 

           _____414______423______________________448______457________468_______478_______488__________501_________________________ 
 2bzd(A) : PFTIPDVALEPGQQVTVPVAVTNQSGIAVPKPSLQLDASPDWQVQGSVEPLMPGRQAKGQVTITVPAGTTPGRYRVGATLRTSAGNASTTFTVTVGLLDQARMSIADVDSEETAREDGRA 
         :                                                                                                                          
 2bzd(C) : PFTIPDVALEPGQQVTVPVAVTNQSGIAVPKPSLQLDASPDWQVQGSVEPLMPGRQAKGQVTITVPAGTTPGRYRVGATLRTSAGNASTTFTVTVGLLDQARMSIADVDSEETAREDGRA 
           _____414______423______________________448______457________468_______478_______488__________501_________________________ 

           ________________________________________________________________________________________________________________________ 
 2bzd(A) : SNVIDGNPSTFWHTEWSRADAPGYPHRISLDLGGTHTISGLQYTRRQNSANEQVADYEIYTSLNGTTWDGPVASGRFTTSLAPQRAVFPARDARYIRLVALSEQTGHKYAAVAELEVEGQ 
         :                                                                                                                          
 2bzd(C) : SNVIDGNPSTFWHTEWSRADAPGYPHRISLDLGGTHTISGLQYTRRQNSANEQVADYEIYTSLNGTTWDGPVASGRFTTSLAPQRAVFPARDARYIRLVALSEQTGHKYAAVAELEVEGQ 
           ________________________________________________________________________________________________________________________ 

           _                                                                                                                        
 2bzd(A) : R                                                                                                                        
         :                                                                                                                          
 2bzd(C) : R                                                                                                                        
           _                                                                                                                        

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
12.1
Translation
(A)
0.5
Closure
(%)
42.4
Bending Residues
( green )
  401 - 402
  488 - 493
Bending Region Analysis
Property Value
Fixed Domain
( blue )
1
Moving Domain
( yellow )
3
Rotation Angle
(deg)
5.5
Translation
(A)
0.2
Closure
(%)
59.3
Bending Residues
( green )
  414 - 415
  423 - 424
  448 - 449
  457 - 458
  468 - 469
  478 - 479
  501 - 502
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

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

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

Movement classification: Shear

PyMOL Script

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