DynDom - Protein Domain Motions

Groel

(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
Conformer 1 (PDB)	1kp8 (A)
Conformer 2 (PDB)	1kp8 (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	155	0.31	30 - 32 90 - 96 127 - 128 137 - 188 378 - 416 445 - 496
2	175	0.38	4 - 29 33 - 89 97 - 126 130 - 136 417 - 444 497 - 523
3	189	0.04	189 - 377

Sequence

`__________________________29_32_______________________________________________________89_____96_________________________` `1kp8(A) : AAKDVKFGNDAGVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGID` `:` `1kp8(B) : AAKDVKFGNDAGVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGID` `__________________________29_32_______________________________________________________89_____96_________________________` `__126___________________________________________________________188_____________________________________________________` `1kp8(A) : KAVTVAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVA` `:` `1kp8(B) : KAVTVAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVA` `__126___________________________________________________________188_____________________________________________________` `________________________________________________________________________________________________________________________` `1kp8(A) : KAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYD` `:` `1kp8(B) : KAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYD` `________________________________________________________________________________________________________________________` `____________376_____________________________________416_________________________444_____________________________________` `1kp8(A) : REKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKLADLRGQNADQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAA` `:` `1kp8(B) : REKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKLADLRGQNADQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAA` `____________376_____________________________________416_________________________444_____________________________________` `____________496______________________________` `1kp8(A) : TEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLPK` `:` `1kp8(B) : TEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLPK` `____________496______________________________`

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)	3.0
Translation (A)	0.3
Closure (%)	72.4
Bending Residues ( green )	29 - 30 32 - 33 89 - 90 96 - 97 126 - 139 416 - 417 444 - 445 496 - 497
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	6.3
Translation (A)	0.5
Closure (%)	71.2
Bending Residues ( green )	188 - 191 376 - 378
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

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

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

Movement classification:

No Contacts

PyMOL Script

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