DynDom - Protein Domain Motions

Pectate Lyase

(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	Pectate Lyase
Conformer 1 (PDB)	2v8i (A)
Conformer 2 (PDB)	2v8j (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	360	0.48	7 - 187 202 - 233 303 - 311 398 - 401 404 - 537
2	171	0.65	188 - 201 234 - 302 312 - 397 402 - 403

Sequence

`________________________________________________________________________________________________________________________` `2v8i(A) : DRLTVVKQYVDNVLNKASDTYHGDKPSPLLADGVDPRTGQQLEWIFPDGRRAVLSNFSAQQNLMRVMSGLSQLSGDPRYQKRAEDIVRYHFQNYQDPSGLLYWGGHRFVDLKTLQPEGPS` `:` `2v8j(A) : RLTVVKQYVDNVLNKASDTYHGDKPSPLLADGVDPRTGQQLEWIFPDGRRAVLSNFSAQQNLMRVMSGLSQLSGDPRYQKRAEDIVRYHFQNYQDPSGLLYWGGHRFVDLKTLQPEGPS` `________________________________________________________________________________________________________________________` `____________________________________________________________186____________201_____________________________233__________` `2v8i(A) : EKEMVHELKNAYPYYDLMFSVDSDATARFIRGFWNAHVYDWRILETSRHGEYGKPMGALWESKFEQQPPFFATKGLSFLNAGNDLIYSASLLYKHQQDQGALTWAKRLADQYVLPRDAKT` `:` `2v8j(A) : EKEMVHELKNAYPYYDLMFSVDSDATARFIRGFWNAHVYDWRILETSRHGEYGKPMGALWESKFEQQPPFFATKGLSFLNAGNDLIYSASLLYKHQQDQGALTWAKRLADQYVLPRDAKT` `____________________________________________________________186____________201_____________________________233__________` `________________________________________________________302______311____________________________________________________` `2v8i(A) : GLGVYQFTQALKREEPTDDADTHSKFGDRAQRQFGPEFGPTALEGNMMLKGRTSTLYSENALMQLQLGKDLGPQGQDLLKWTVDGLKAFAKYAYNDQDNTFRPMIANGQDLSNYTLPRDG` `:` `2v8j(A) : GLGVYQFTQALKREEPTDDADTHSKFGDRAQRQFGPEFGPTALEGNMMLKGRTSTLYSENALMQLQLGKDLGPQGQDLLKWTVDGLKAFAKYAYNDQDNTFRPMIANGQDLSNYTLPRDG` `________________________________________________________302______311____________________________________________________` `______________________________396_______________________________________________________________________________________` `2v8i(A) : YYGKKGTVLKPYKAGNEFLISYARAYAIDNDPLLWKVARGIANDQGLGDIGTAPGKEVKVNMDTTNSDPYALFALLDLYHASQVADYRKLAEKIGDNIIKIRYIDGFFMASSDRQYADVD` `:` `2v8j(A) : YYGKKGTVLKPYKAGNEFLISYARAYAIDNDPLLWKVARGIANDQGLGDIGTAPGKEVKVNMDTTNSDPYALFALLDLYHASQVADYRKLAEKIGDNIIKIRYIDGFFMASSDRQYADVD` `______________________________396_______________________________________________________________________________________` `_______________________________________________________________` `2v8i(A) : AIEPYALLALEASLRNKPQAVAPFLNGAGFTEGAYRMDDGSARVSTRDNELFLLNVGEKLQPN` `:` `2v8j(A) : AIEPYALLALEASLRNKPQAVAPFLNGAGFTEGAYRMDDGSARVSTRDNELFLLNV******` `_______________________________________________________________`

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)	12.9
Translation (A)	0.3
Closure (%)	97.6
Bending Residues ( green )	186 - 188 201 - 202 233 - 234 302 - 307 311 - 319 396 - 404
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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