DynDom - Protein Domain Motions

Polyprotein

(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	Polyprotein
Conformer 1 (PDB)	1nb4 (A)
Conformer 2 (PDB)	1gx6 (A)
Window Length	9
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	403	0.95	6 - 21 34 - 390 415 - 418 420 - 430 457 - 470 472 - 472 491 - 492 495 - 502
2	108	0.63	22 - 33 391 - 413 419 - 419 431 - 456 471 - 471 473 - 490 493 - 494 503 - 527

Sequence

`___________________21__________33_______________________________________________________________________________________` `1nb4(A) : SMSYTWTGALITPCAAEESKLPINPLSNSLLRHHNMVYATTSRSASLRQKKVTFDRLQVLDDHYRDVLKEMKAKASTVKAKLLSIEEACKLTPPHSAKSKFGYGAKDVRNLSSRAVNHIR` `:` `1gx6(A) : SsYTWTGALITPCAAEESKLPINALSNSLLRHHN-vYATTSRSAGLRQKKVTFDRLQVLDDHYRDVLKE-kAKASTVKAKLLSVEEACKLTPPHSAKSKFGYGAKDVRNLSSKAVNHIH` `___________________21__________33_______________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1nb4(A) : SVWEDLLEDTETPIDTTIMAKSEVFCVQPEKGGRKPARLIVFPDLGVRVCEKMALYDVVSTLPQAVMGSSYGFQYSPKQRVEFLVNTWKSKKCPMGFSYDTRCFDSTVTESDIRVEESIY` `:` `1gx6(A) : SVWKDLLEDTVTPIDTTI-aKNEVFCVQPEKGGRKPARLIVFPDLGVRVCEK-aLYDVVSTLPQ-VVgSSYGFQYSPGQRVEFLVNTWKSKKNP-gFSYDTRCFDSTVTENDIRVEESIY` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1nb4(A) : QCCDLAPEARQAIRSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKATAACRAAKLQDCTMLVNGDDLVVICESAGTQEDAAALRAFTEAMTRYSAPPGDPPQPEYDL` `:` `1gx6(A) : QCCDLAPEARQAIKSLTERLYIGGPLTNSKGQNCGYRRCRASGVLTTSCGNTLTCYLKASAACRAAKLQDCT-lVNGDDLVVICESAGTQEDAASLRVFTEA-tRYSAPPGDPPQPEYDL` `________________________________________________________________________________________________________________________` `___________________________390____________________413__418___________________________________456___________470__________` `1nb4(A) : ELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPINSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFTLHSYSPG` `:` `1gx6(A) : ELITSCSSNVSVAHDASGKRVYYLTRDPTTPLARAAWETARHTPVNSWLGNII-yAPTLWAR--iLtHFFSILLAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFSLHSYSPG` `___________________________390____________________413__418___________________________________456___________470__________` `_______490_________502________________________________________________________________` `1nb4(A) : EINRVASCLRKLGVPPLRTWRHRARSVRAKLLSQGGRAATCGRYLFNWAVRTKLKLTPIPAASQLDLSGWFVAGYSGGDIYHSLSR` `:` `1gx6(A) : EINRVASCLRKLGVPPLRVWRHRARSVRARLLSQGGRAATCGKYLFNWAVK**********************************` `_______490_________502________________________________________________________________`

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)	7.5
Translation (A)	-0.2
Closure (%)	97.3
Bending Residues ( green )	21 - 22 33 - 34 390 - 391 413 - 415 418 - 431 456 - 461 470 - 473 490 - 495 502 - 503
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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