DynDom - Protein Domain Motions

Ovotransferrin

(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	Ovotransferrin
Conformer 1 (PDB)	1ryx (A)
Conformer 2 (PDB)	2d3i (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	341	1.49	7 - 91 250 - 330 345 - 421 472 - 475 590 - 683
2	158	1.21	92 - 247 331 - 332
3	153	0.91	433 - 471 476 - 589

Sequence

`________________________________________________________________________________________90______________________________` `1ryx(A) : APPKSVIRWCTISSPEEKKCNNLRDLTQQERISLTCVQKATYLDCIKAIANNEADAISLDGGQAFEAGLAPYKLKPIAAEVYEHTEGSTTSYYAVAVVKKGTEFTVNDLQGKTSCHTGLG` `:` `2d3i(A) : ****SVIRWCTISSPEEKKCNNLRDLTQQERISLTCVQKATYLDCIKAIANNEADAISLDGGQVFEAGLAPYKLKPIAAEVYEHTEGSTTSYYAVAVVKKGTEFTVNDLQGKTSCHTGLG` `________________________________________________________________________________________90______________________________` `________________________________________________________________________________________________________________________` `1ryx(A) : RSAGWNIPIGTLLHRGAIEWEGIESGSVEQAVAKFFSASCVPGATIEQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTTVNENAPDQKDEYELLCLDGSRQPVDNYK` `:` `2d3i(A) : RSAGWNIPIGTLIHRGAIEWEGIESGSVEQAVAKFFSASCVPGATIEQKLCRQCKGDPKTKCARNAPYSGYSGAFHCLKDGKGDVAFVKHTTVNENAPDQKDEYELLCLDGSRQPVDNYK` `________________________________________________________________________________________________________________________` `____247____________________________________________________________________________326__________________________________` `1ryx(A) : TCNWARVAAHAVVARDDNKVEDIWSFLSKAQSDFGVDTKSDFHLFGPPGKKDPVLKDLLFKDSAIMLKRVPSLMDSQLYLGFEYYSAIQSMRKDQLTPSPRENRIQWCAVGKDEKSKCDR` `:` `2d3i(A) : TCNWARVAAHAVVARDDNKVEDIWSFLSKAQSDFGVDTKSDFHLFGPPGKKDPVLKDLLFKDSAIMLKRVPSLMDSQLYLGFEYYSAIQSMRKDQ------eNRIQWCAVGKDEKSKCDR` `____247____________________________________________________________________________326__________________________________` `__________________________________________________________421_______________________________________________471_________` `1ryx(A) : WSVVSNGDVECTVVDETKDCIIKIMKGEADAVALDGGLVYTAGVCGLVPVMAERYDDESQCSKTDERPASYFAVAVARKDSNVNWNNLKGKKSCHTAVGRTAGWVIPMGLIHNRTGTCNF` `:` `2d3i(A) : WSVVSNGDVECTVVDETKDCIIKIMKGEADAVALDGGLVYTAGVCGLVPVMAERYDDESQC------pASYFAVAVARKDSNVNWNNLKGKKSCHTAVGRTAGWVIPMGLIHNRTGTCNF` `__________________________________________________________421_______________________________________________471_________` `__________________________________________________________________________________________________________589___________` `1ryx(A) : DEYFSEGCAPGSPPNSRLCQLCQGSGGIPPEKCVASSHEKYFGYTGALRCLVEKGDVAFIQHSTVEENTGGKNKADWAKNLQMDDFELLCTDGRRANVMDYRECNLAEVPTHAVVVRPEK` `:` `2d3i(A) : DEYFSEGCAPGSPPNSRLCQLCQGSGGIPPEKCVASSHEKYFGYTGALRCLVEKGDVAFIQHSTVEENTGGKNKADWAKNLQMDDFELLCTDGRRANVMDYRECNLAEVPTHAVVVRPEK` `__________________________________________________________________________________________________________589___________` `______________________________________________________________________________________` `1ryx(A) : ANKIRDLLERQEKRFGVNGSEKSKFMMFESQNKDLLFKDLTKCLFKVREGTTYKEFLGDKFYTVISSLKTCNPSDILQMCSFLEGK` `:` `2d3i(A) : ANKIRDLLERQEKRFGVNGSEKSKFMMFESQNKDLLFKDLTKCLFKVREGTTYKEFLGDKFYTVISSLKTCNPSDILQMCSFLEGK` `______________________________________________________________________________________`

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)	51.4
Translation (A)	-2.1
Closure (%)	89.6
Bending Residues ( green )	90 - 92 247 - 250 326 - 345
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	32.7
Translation (A)	-0.1
Closure (%)	99.8
Bending Residues ( green )	421 - 433 471 - 476 589 - 590
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

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

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

Movement classification: Hinge

PyMOL Script

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