Beta-Agarase B

(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 Beta-Agarase B
  Conformer 1
(PDB) 		4atf (B)
  Conformer 2
(PDB) 		1o4z (D)
  Window Length 5
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)		 Residues
1 270 0.39   62 - 216   228 - 281   291 - 351
2 20 0.4   217 - 227   282 - 290

Sequence


           ________________________________________________________________________________________________________________________ 
 4atf(B) : VDWKDIPVPADAGPNMKWEFQEISDNFEYEAPADNKGSEFLEKWDDFYHNAWAGPGLTEWKRDRSYVADGELKMWATRKPGSDKINMGCITSKTRVVYPVYIEARAKVMNSTLASDVWLL 
         :                                                                                                                          
 1o4z(D) : VDWKDIPVPADAGPNMKWEFQEISDNFEYEAPADNKGSEFLEKWDDFYHNAWAGPGLTEWKRDRSYVADGELKMWATRKPGSDKINMGCITSKTRVVYPVYIEARAKVMNSTLASDVWLL 
           ________________________________________________________________________________________________________________________ 

           ____________________________________216________227___________________________________________________281____288_________ 
 4atf(B) : SADDTQEIDILDAYGADYSESAGKDHSYFSKKVHISHHVFIRDPFQDYQPKDAGSWFEDGTVWNKEFHRFGVYWRDPWHLEYYIDGVLVRTVSGKDIIDPKHFTNTTDPGNTEIDTRTGL 
         :                                                                                                                          
 1o4z(D) : SADDTQEIDILEAYGADYSESAGKDHSYFSKKVHISHHVFIRDPFQDYQPKDAGSWFEDGTVWNKEFHRFGVYWRDPWHLEYYIDGVLVRTVSGKDIIDPKHFTNTTDPGNTEIDTRTGL 
           ____________________________________216________227___________________________________________________281____288_________ 

           _________________________________________________________                                                                
 4atf(B) : NKEMDIIINTEDQTWRSSPASGLQSNTYTPTDNELSNIENNTFGVDWIRIYKPVEK*                                                                
         :                                                                                                                          
 1o4z(D) : NKEMDIIINTEDQTWRSSPASGLQSNTYTPTDNELSNIENNTFGVDWIRIYKPVEKL                                                                
           _________________________________________________________                                                                

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Domain Pairs

Property Value
Fixed Domain
( blue ) 		1
Moving Domain
( red ) 		2
Rotation Angle
(deg) 		4.1
Translation
(A) 		-0.2
Closure
(%) 		98.8
Bending Residues
( green ) 		  216 - 217
  227 - 228
  281 - 282
  288 - 292
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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