D-Alanine--D-Alanine 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 D-Alanine--D-Alanine Ligase
  Conformer 1
(PDB)
2yzg (B)
  Conformer 2
(PDB)
2zdq (A)
  Window Length 9
  Minimum ratio 1.0
  Minimum domain size 20

Domains

Domain Size Backbone RMSD
(A)
Residues
1 219 1.72   6 - 109   126 - 127   193 - 315
2 80 0.73   110 - 125   128 - 192

Sequence


           __________________________________________________________________________________________________________109___________ 
 2yzg(B) : *RVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALC-dKDLSK 
         :                                                                                                                          
 2zdq(A) : MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSK 
           __________________________________________________________________________________________________________109___________ 

           __125________________________________________________________________192________________________________________________ 
 2yzg(B) : RVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPF--------pGRAELLIPA 
         :                                                                                                                          
 2zdq(A) : RVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPA 
           __125________________________________________________________________192________________________________________________ 

           _______________________________________________________________________________                                          
 2yzg(B) : PLDPGTQETVQELALKAYKVLGVRG-aRVDFFLAEGELYLNELNTIPGFTPTS-yPRLFEAGGVAYPELLRRLVELALT                                          
         :                                                                                                                          
 2zdq(A) : PLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT                                          
           _______________________________________________________________________________                                          

Morph

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Domain Pairs

Property Value
Fixed Domain
( blue )
1
Moving Domain
( red )
2
Rotation Angle
(deg)
13.3
Translation
(A)
-0.6
Closure
(%)
82.3
Bending Residues
( green )
  109 - 116
  125 - 128
  192 - 193
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

PyMOL Script

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