DynDom - Protein Domain Motions

Groel (Hsp60 Class)

(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 (Hsp60 Class)
Conformer 1 (PDB)	1gr5 (H)
Conformer 2 (PDB)	2c7e (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	87	0.8	138 - 194 376 - 407
2	247	0.4	4 - 135 408 - 524
3	179	1.25	195 - 375

Sequence

`________________________________________________________________________________________________________________________` `1gr5(H) : AAKDVKFGNDAGVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGID` `:` `2c7e(A) : AAKDVKFGNDAGVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGID` `________________________________________________________________________________________________________________________` `__________134_____________________________________________________190___________________________________________________` `1gr5(H) : KAVTVAVEELKALS--cSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDGTGLQDELDVVE--qFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVA` `:` `2c7e(A) : KAVTVAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDGTGLQDELDVVEgMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVA` `__________134_____________________________________________________190___________________________________________________` `________________________________________________________________________________________________________________________` `1gr5(H) : KAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYD` `:` `2c7e(A) : KAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYD` `________________________________________________________________________________________________________________________` `_______371_________________________________407__________________________________________________________________________` `1gr5(H) : REKLQERVAKL--gVAVIKVGAATEVEMKEKKARVEDALHATRAAVE--vVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAA` `:` `2c7e(A) : REKLQERVAKLAgGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAA` `_______371_________________________________407__________________________________________________________________________` `_____________________________________________` `1gr5(H) : TEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLPK` `:` `2c7e(A) : TEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLPK` `_____________________________________________`

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)	27.9
Translation (A)	-3.5
Closure (%)	86.4
Bending Residues ( green )	134 - 139 407 - 412
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	19.9
Translation (A)	5.3
Closure (%)	99.0
Bending Residues ( green )	190 - 195 371 - 376
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: Hinge

PyMOL Script

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