DynDom - Protein Domain Motions

Receptor Protein-Tyrosine Kinase Erbb-2

(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	Receptor Protein-Tyrosine Kinase Erbb-2
Conformer 1 (PDB)	1n8z (C)
Conformer 2 (PDB)	1s78 (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	164	0.89	279 - 413 418 - 421 424 - 428 430 - 440 446 - 451 458 - 465 474 - 475
2	285	1.0	4 - 278 414 - 417 422 - 423 441 - 445 466 - 473
3	107	0.82	429 - 429 452 - 457 476 - 575

Sequence

`________________________________________________________________________________________________________________________` `1n8z(C) : TQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLsPGGLRELQLRSLTEILKG` `:` `1s78(B) : TQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLsPGGLRELQLRSLTEILKG` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1n8z(C) : GVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPAL` `:` `1s78(B) : GVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPAL` `________________________________________________________________________________________________________________________` `__________________________278___________________________________________________________________________________________` `1n8z(C) : VTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTA---tQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFD----sNTAP` `:` `1s78(B) : VTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAP` `__________________________278___________________________________________________________________________________________` `_________________________________________413_417_421_425____________440__445___451___457_____465_____473________________` `1n8z(C) : LQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLAC` `:` `1s78(B) : LQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLAC` `_________________________________________413_417_421_425____________440__445___451___457_____465_____473________________` `____________________________________________________________________________________________________________` `1n8z(C) : HQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSiWKFPDEEGACQPCPIN` `:` `1s78(B) : HQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVAR********************` `____________________________________________________________________________________________________________`

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)	8.5
Translation (A)	0.1
Closure (%)	73.6
Bending Residues ( green )	278 - 279 413 - 414 417 - 418 421 - 424 440 - 441 445 - 446 465 - 466 473 - 474
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	10.7
Translation (A)	0.6
Closure (%)	100.0
Bending Residues ( green )	425 - 430 451 - 452 457 - 458 475 - 482
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: Mixed

PyMOL Script

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