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)
1w8n (A)
  Conformer 2
(PDB)
2bzd (A)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 94 0.46   403 - 414   417 - 417   420 - 500
2 353 0.39   50 - 402
3 149 0.34   415 - 416   418 - 419   501 - 645

Sequence


           ________________________________________________________________________________________________________________________ 
 1w8n(A) : GEPLYTEQDLAVNGREGFPNYRIPALTVTPDGDLLASYDGRPTGIGAPGPNSILQRRSTDGGRTWGEQQVVSAGQTTAPIKGFSDPSYLVDRETGTIFNFHVYSQRQGFAGSRPGTDPAD 
         :                                                                                                                          
 2bzd(A) : GEPLYTEQDLAVNGREGFPNYRIPALTVTPDGDLLASYDGRPTGIDAPGPNSILQRRSTDGGRTWGEQQVVSAGQTTAPIKGFSDPSYLVDRETGTIFNFHVYSQRQGFAGSRPGTDPAD 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________________ 
 1w8n(A) : PNVLHANVATSTDGGLTWSHRTITADITPDPGWRSRFAASGEGIQLRYGPHAGRLIQQYTIINAAGAFQAVSVYSDDHGRTWRAGEAVGVGMDENKTVELSDGRVLLNSRDSARSGYRKV 
         :                                                                                                                          
 2bzd(A) : PNVLHANVATSTDGGLTWSHRTITADITPDPGWRSRFAASGEGIQLRYGPHAGRLIQQYTIINAAGAFQAVSVYSDDHGRTWRAGEAVGVGMDANKTVELSDGRVLLNSRDSARSGYRKV 
           ________________________________________________________________________________________________________________________ 

           ________________________________________________________________________________________________________________401_____ 
 1w8n(A) : AVSTDGGHSYGPVTIDRDLPDPTNNASIIRAFPDAPAGSARAKVLLFSNAASQTSRSQGTIRMSCDDGQTWPVSKVFQPGSMSYSTLTALPDGTYGLLYEPGTGIRYANFNLAWLGGICA 
         :                                                                                                                          
 2bzd(A) : AVSTDGGHSYGPVTIDRDLPDPTNNASIIRAFPDAPAGSARAKVLLFSNAASQTSRSQGTIRMSCDDGQTWPVSKVFQPGSMSYSTLTALPDGTYGLLYEPGTGIRYANFNLAWLGGICA 
           ________________________________________________________________________________________________________________401_____ 

           _____414___________________________________________________________________________________500__________________________ 
 1w8n(A) : PFTIPDVALEPGQQVTVPVAVTNQSGIAVPKPSLQLDASPDWQVQGSVEPLMPGRQAKGQVTITVPAGTTPGRYRVGATLRTSAGNASTTFTVTVGLLDQARMSIADVDSEETAREDGRA 
         :                                                                                                                          
 2bzd(A) : PFTIPDVALEPGQQVTVPVAVTNQSGIAVPKPSLQLDASPDWQVQGSVEPLMPGRQAKGQVTITVPAGTTPGRYRVGATLRTSAGNASTTFTVTVGLLDQARMSIADVDSEETAREDGRA 
           _____414___________________________________________________________________________________500__________________________ 

           ________________________________________________________________________________________________________________________ 
 1w8n(A) : SNVIDGNPSTFWHTEWSRADAPGYPHRISLDLGGTHTISGLQYTRRQNSANEQVADYEIYTSLNGTTWDGPVASGRFTTSLAPQRAVFPARDARYIRLVALSEQTGHKYAAVAELEVEGQ 
         :                                                                                                                          
 2bzd(A) : SNVIDGNPSTFWHTEWSRADAPGYPHRISLDLGGTHTISGLQYTRRQNSANEQVADYEIYTSLNGTTWDGPVASGRFTTSLAPQRAVFPARDARYIRLVALSEQTGHKYAAVAELEVEGQ 
           ________________________________________________________________________________________________________________________ 

           _                                                                                                                        
 1w8n(A) : R                                                                                                                        
         :                                                                                                                          
 2bzd(A) : R                                                                                                                        
           _                                                                                                                        

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
12.9
Translation
(A)
0.7
Closure
(%)
17.4
Bending Residues
( green )
  401 - 403
Bending Region Analysis
Property Value
Fixed Domain
( blue )
1
Moving Domain
( yellow )
3
Rotation Angle
(deg)
9.5
Translation
(A)
0.2
Closure
(%)
82.6
Bending Residues
( green )
  414 - 420
  500 - 503
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:

No Contacts

PyMOL Script

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