DynDom - Protein Domain Motions

Ns5 Rdrp

(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	Ns5 Rdrp
Conformer 1 (PDB)	5wz3 (A)
Conformer 2 (PDB)	5u04 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	249	1.9	367 - 510 524 - 708
2	211	0.49	323 - 366 511 - 523 709 - 885

Sequence

`_______________________________________________________________________________366______________________________________` `5wz3(A) : HMKIIGNRIERIRSEHAETWFFDENHPYRTWAYHGSYEAPlINGVVRLLSKPWDVVTGVTGItTPYGQQRVFKEKVDTRVPDPQEGTRQVMSMVSSWLWKELGKHKRPRVCTKEEFINKV` `:` `5u04(A) : ****************************************LVNGVVRLLSKPWDVVTGVT-------------------vPDPQEGTRQVMNIVSSWLWKELGKRKRPRVCTKEEFINKV` `_______________________________________________________________________________366______________________________________` `_______________________________________________________________________________510__________523_________________________` `5wz3(A) : RS----------eAVNDPRFWALVDKEREHHLRGECQSCVYN----MwYMWLGARFLEFEALGFLNEDHWMGRENSGGGVEGLGLQRLGYVLEEMSRIPGGRMYADDTAGWDTRISRFDL` `:` `5u04(A) : RSNAeKEWKTAVEAVNDPRFWALVDREREHHLRGECHSCVYNgSRAIWYMWLGARFLEFEALGFLNEDHWMGRENSGGGVEGLGLQRLGYILEEMNRAPGGKMYA--------rISKFDL` `_______________________________________________________________________________510__________523_________________________` `________________________________________________________________________________________________________________________` `5wz3(A) : ENEALITNQMEKGHRALALAIIKYTYQNKVVKVLRPAEKGKTVMDIISRQDQRGSGQVVTYALNTFTNLVVQLIRNMEAEEVLEMQDLWLLRRSEKVTNWLQSNGWDRLKRMAVSGDDCV` `:` `5u04(A) : ENEALITNQMEEGHRTLALAVIKYTYQN-----------------------------vVTYALNTFTNLVVQLIRNMEAEEVLEMQDLWLLRKPEKVTRWLQSNGWDRLKRMAVSGDDCV` `________________________________________________________________________________________________________________________` `_____________________________________708________________________________________________________________________________` `5wz3(A) : VKPIDDRFAHALRFLNDMGKVRKDTQEWKPSTGWDNWEEVPFCSHHFNKLHLKDGRSIVVPCRHQDELIGRARVSPGAGWSIRETACLAKSYAQMWQLLYFHRRDLRLMANAICSSVPVD` `:` `5u04(A) : VKPIDDRFAHALRFLNDMGKV-----eWKPSTGWSNWEEVPFCSHHFNKLYLKDGRSIVVPCRHQDELIGRARVSPGAGWSIRETACLAKSYAQMWQLLYFHRRDLRLMANAICSAVPVD` `_____________________________________708________________________________________________________________________________` `___________________________________________________________________________________________________` `5wz3(A) : WVPTGRTTWSIHGKGEWMTTEDMLVVWNRVWIEENDHMEDKTPVTKWTDIPYLGKREDLWCGSLIGHRPRTTWAENIKNTVNMVRRIIGDEEKYMDYLS` `:` `5u04(A) : WVPTGRTTWSIHGKGEWMTTEDMLMVWNRVWIEENDHMEDKTPVTKWTDIPYLGKREDLWCGSLIGHRPRTTWAENIKDTVNMVRRIIGDEEKYMDYLS` `___________________________________________________________________________________________________`

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)	10.6
Translation (A)	0.3
Closure (%)	23.9
Bending Residues ( green )	366 - 367 510 - 512 523 - 524 708 - 709
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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