DynDom - Protein Domain Motions

Groel Protein

(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	Groel Protein
Conformer 1 (PDB)	1kp8 (F)
Conformer 2 (PDB)	1pcq (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	89	1.32	138 - 191 374 - 408
2	249	1.09	4 - 137 409 - 523
3	182	0.7	192 - 373

Sequence

`________________________________________________________________________________________________________________________` `1kp8(F) : AAKDVKFGNDAGVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGID` `:` `1pcq(A) : AAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGID` `________________________________________________________________________________________________________________________` `____________136__________________________________________________189____________________________________________________` `1kp8(F) : KAVTVAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVA` `:` `1pcq(A) : KAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVA` `____________136__________________________________________________189____________________________________________________` `________________________________________________________________________________________________________________________` `1kp8(F) : KAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYD` `:` `1pcq(A) : KAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYD` `________________________________________________________________________________________________________________________` `_________373________________________________408_________________________________________________________________________` `1kp8(F) : REKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKLADLRGQNADQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAA` `:` `1pcq(A) : REKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAA` `_________373________________________________408_________________________________________________________________________` `_____________________________________________` `1kp8(F) : TEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLPK` `:` `1pcq(A) : TEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLP*` `_____________________________________________`

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)	28.4
Translation (A)	0.8
Closure (%)	95.7
Bending Residues ( green )	136 - 138 408 - 409
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	87.4
Translation (A)	0.0
Closure (%)	3.5
Bending Residues ( green )	189 - 193 373 - 374
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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