DynDom - Protein Domain Motions

Nicotinamide Phosphoribosyltransferase

(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	Nicotinamide Phosphoribosyltransferase
Conformer 1 (PDB)	2gvl (A)
Conformer 2 (PDB)	2gvg (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	250	0.56	11 - 41 58 - 123 128 - 161 209 - 209 218 - 226 232 - 241 384 - 482
2	206	0.44	54 - 57 124 - 127 162 - 208 210 - 217 227 - 231 242 - 383

Sequence

`_______________________________41__57_______________________________________________________________123_127_____________` `2gvl(A) : FNILLATDSYKVTHYKQYPPNTSKVYSYFECREyEETVFYGLQYILNKYLKGKVVTKEKIQEAKEVYREHFQDDVFNERGWNYILEKYDGHLPIEVKAVPEGSVIPRGNVLFTVENTDPE` `:` `2gvg(A) : FNILLATDSYKVTHYKQYPPNTSKVYSYFECREyEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPE` `_______________________________41__57_______________________________________________________________123_127_____________` `__________________161____________________________________________208______217______226__231_______241___________________` `2gvl(A) : CYWLTNWIETILVQSWYPITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGIALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKD` `:` `2gvg(A) : CYWLTNWIETILVQSWYPITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKD` `__________________161____________________________________________208______217______226__231_______241___________________` `________________________________________________________________________________________________________________________` `2gvl(A) : AFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTEAPLIIRPDSGNPLDTVLKVLDILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEG-kQKKWSIENVSF` `:` `2gvg(A) : AFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVT---kGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAF` `________________________________________________________________________________________________________________________` `383_____________________________________________________________________________________________________` `2gvl(A) : GSGGALLQKLTRDLLNCSFKCSYVVTNGLGVNVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGHDLLHTVFKNGKVTKSYSFDEVRKNAQLNI` `:` `2gvg(A) : GSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNI` `383_____________________________________________________________________________________________________`

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)	4.5
Translation (A)	0.0
Closure (%)	25.2
Bending Residues ( green )	41 - 54 57 - 58 123 - 124 127 - 128 161 - 162 208 - 210 217 - 218 226 - 229 231 - 232 241 - 242 383 - 384
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

PyMOL Script

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