DynDom - Protein Domain Motions

Putative Sam-Dependent RNA Methyltransferase

(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	Putative Sam-Dependent RNA Methyltransferase
Conformer 1 (PDB)	2cww (A)
Conformer 2 (PDB)	1wxx (D)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	122	0.51	4 - 74 77 - 82 90 - 90 92 - 95 99 - 104 170 - 201 357 - 363 371 - 371
2	78	0.66	75 - 76 83 - 89 91 - 91 96 - 98 105 - 169
3	168	0.54	202 - 356 364 - 370 372 - 380

Sequence

`________________________________________________________________________74______82___________95_98___104________________` `2cww(A) : MRIQVNAKGAARLLSRHLWVFRRDVVSGPETPGLYPVYWGRRFLALALYNPHTDLAVRAYRFAPAEDPVAALLENLAQALARREAVLRQDPEGGYRLVHAEGDLLPGLVVDYYAGHAVVQ` `:` `1wxx(D) : *RIQVNAKGAARLLSRHLWVFRRDVVSGPETPGLYPVYWGRRFLALALYNPHTDLAVRAYRFAPAEDPVAALLENLAQALARREAVLRQDPEGGYRLVHAEGDLLPGLVVDYYAGHAVVQ` `________________________________________________________________________74______82___________95_98___104________________` `______________________________________________169_____________________________201_______________________________________` `2cww(A) : ATAHAWEGLLPQVAEALRPHVQSVLAKNDARTRELEGLPLYVRPLLGEVPERVQVQEGRVRYLVDL------gAYLDQRENRLYMERFRGERALDVFSYAGGFALHLALGFREVVAVDSS` `:` `1wxx(D) : ATAHAWEGLLPQVAEALRPHVQSVLAKNDARTRELEGLPLYVRPLLGEVPERVQVQEGRVRYLVDLRAGQKTGAYLDQRENRLY-eRFRGERALDVFSYAGGFALHLALGFREVVAVDSS` `______________________________________________169_____________________________201_______________________________________` `_________________________________________________________________________________________________________________356____` `2cww(A) : AEALRRAEENARLNGLGNVRVLEANAFDLLRRLEKEGERFDLVVLDPPAFAKGKKDVERAYRAYKEVNLRAIKLLKEGGILATASCSHHMTEPLFYAMVAEAAQDAHRLLRVVEKRGQPF` `:` `1wxx(D) : AEALRRAEENARLNGLGNVRVLEANAFDLLRRLEKEGERFDLVVLDPPAFAKGKKDVERAYRAYKEVNLRAIKLLKEGGILATASCSHH-tEPLFYA-vAEAAQDAHRLLRVVEKRGQPF` `_________________________________________________________________________________________________________________356____` `363____370____________` `2cww(A) : DHPVLLNHPETHYLKFAVFQVL` `:` `1wxx(D) : DHPVLLNHPETHYLKFAVFQVL` `363____370____________`

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)	6.4
Translation (A)	0.1
Closure (%)	12.2
Bending Residues ( green )	74 - 77 82 - 92 95 - 96 98 - 99 104 - 105 169 - 170
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	7.5
Translation (A)	0.4
Closure (%)	8.0
Bending Residues ( green )	201 - 202 356 - 357 363 - 364 370 - 372
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: Shear

PyMOL Script

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