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)	1ss8 (A)
Conformer 2 (PDB)	1sx3 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	338	0.65	71 - 76 80 - 84 92 - 98 100 - 100 102 - 104 136 - 406 443 - 447 450 - 470 474 - 480 485 - 492 508 - 511
2	182	0.6	4 - 70 77 - 79 85 - 91 99 - 99 101 - 101 105 - 135 407 - 442 448 - 449 471 - 473 481 - 484 493 - 507 512 - 523

Sequence

`___________________________________________________________________70__74_______________91_____98___104_________________` `1ss8(A) : AAKDVKFGNDAGVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGID` `:` `1sx3(A) : AAKDVKFGNDAGVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGID` `___________________________________________________________________70__74_______________91_____98___104_________________` `___________135__________________________________________________________________________________________________________` `1ss8(A) : KAVTVAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVA` `:` `1sx3(A) : KAVTVAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVA` `___________135__________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1ss8(A) : KAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYD` `:` `1sx3(A) : KAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYD` `________________________________________________________________________________________________________________________` `__________________________________________406_________________________________442__447____________________470______479__` `1ss8(A) : REKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAA` `:` `1sx3(A) : REKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAA` `__________________________________________406_________________________________442__447____________________470______479__` `484____491_____________507_511_______________` `1ss8(A) : TEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLP*` `:` `1sx3(A) : TEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLPK` `484____491_____________507_511_______________`

Morph

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Status: Initialising

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	8.7
Translation (A)	-0.1
Closure (%)	99.9
Bending Residues ( green )	108 - 110 217 - 219 257 - 259
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	5.3
Translation (A)	-0.1
Closure (%)	13.8
Bending Residues ( green )	114 - 115 191 - 192
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification:

No Contacts

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

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

Movement classification: Shear

PyMOL Script

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