DynDom - Protein Domain Motions

Rap Guanine Nucleotide Exchange Factor 4

(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	Rap Guanine Nucleotide Exchange Factor 4
Conformer 1 (PDB)	2byv (E)
Conformer 2 (PDB)	3cf6 (E)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	484	2.18	443 - 443 445 - 988
2	132	2.57	312 - 442 444 - 444

Sequence

`________________________________________________________________________________________________________________________` `2byv(E) : WIACLDKRPLERSSEDVDIIFTRLKGVKAFEKFHPNLLRQICLCGYYENLEKGITLFRQGDIGTNWYAVLAGSLDVKVSETSSHQDAVTICTLGIGTAFGESILDNTPRHATIVTRESSE` `:` `3cf6(E) : **********************************************************************************************************************` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2byv(E) : LLRIEQEDFKALWEKYRQYMAGLLAPPYGVMETGSNnVPSEKILRAGKILRIAILSRAPHMIRDRKYHLKTYRQCCVGTELVDWMIQQTSCVHSRTQAVGMWQVLLEDGVLNHVDQERHF` `:` `3cf6(E) : ********************************************************************************************************************` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2byv(E) : QDKYLFYRFLDDEREDAPLPTEEEKKECDEELQDTMLLLSQMGPDAHMRMILRKPPGQRTVDDLEIIYDELLHIKALSHLSTTVKRELAGVLIFESHAKGGTVLFNQGEEGTSWYIILKG` `:` `3cf6(E) : ********************************************MRMILRKPPGQRTVDDLEIIYDELLHIKALSHLSTTVKRELAGVLIFESHAKGGTVLFNQGEEGTSWYIILKG` `________________________________________________________________________________________________________________________` `____________________________________________________437_________________________________________________________________` `2byv(E) : SVNVVIYGKGVVCTLHEGDDFGKLALVNDAPRAASIVLREDNCHFLRVDKEDFNRILRDVEANTVRLKEHDQDVLVLEKVPAqQKYTVMSGTPEKILEHFLETIRLEPSLNEATDSVLND` `:` `3cf6(E) : SVNVVIYGKGVVCTLHEGDDFGKLALVNDAPRAASIVLREDNCHFLRVDKEDFNRILRDVEANTVRLKEHDQDVLVLEKV---qKYTVMSGTPEKILEHFLETIRLEPSLNEATDSVLND` `____________________________________________________437_________________________________________________________________` `________________________________________________________________________________________________________________________` `2byv(E) : FVMMHCVFMPNTQLCPALVAHYHAQPSQGTEQERMDYALNNKRRVIRLVLQWAAMYGDLLQEDDVAMAFLEEFYVSVSDDARMMAAFKEQLPELEKIVKkRQPIRGSDEVLFKVYCIDHT` `:` `3cf6(E) : FVMMHCVFMPNTQLCPALVAHYHAQPSQGTEQERMDYALNNKRRVIRLVLQWAAMYGDLLQEDDVAMAFLEEFYVSVSDDARMMAAFKEQLPELEKIV--rQPIRGSDEVLFKVYCIDHT` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2byv(E) : YTTIRVPVAASVKEVISAVADKLGSGEGLIIVKMNSGGEKVVLKSNDVSVFTTLTINGRLFA-------sLTPLPEQEGPTTGTVGTFELMSSKDLAYQMTTYDWELFNCVHELELIYHT` `:` `3cf6(E) : YTTIRVPVAASVKEVISAVADKLGSGEGLIIVKMNSGGEKVVLKSNDVSVFTTLTINGRLFACPREQFDSLTPLPEQEGPTTGTVGTFELMSSKDLAYQMTTYDWELFNCVHELELIYHT` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `2byv(E) : FGRHNFKKTTANLDLFLRRFNEIQFWVVTEVCLCSQLSKRVQLLKKFIKIAAHCKEYKNLNSFFAIVMGLSNVAVSRLALTWEKLPSKFKKFYAEFESLMDPSRNHRAYRLTAAKLEPPL` `:` `3cf6(E) : FGRHNFKKTTANLDLFLRRFNEIQFWVVTEVCLCSQLSKRVQLLKKFIKIAAHCKEYKNLNSFFAIVMGLSNVAVSRLALTWEKLPSKFKKFYAEFESLMDPSRNHRAYRLTAAKLEPPL` `________________________________________________________________________________________________________________________` `_________________________________________________________________________________________` `2byv(E) : IPFMPLLIKDMTFTHEGNKTFIDNLVNFEKMRMIANTARTVRYYRSQPFNPDAAQANKNHQDVRSYVRQLNVIDNQRTLSQMSHRLEPR` `:` `3cf6(E) : IPFMPLLIKDMTFTHEGNKTFIDNLVNFEKMRMIANTARTVRYYRSQPF---------NhQDVRSYVRQLNVIDNQRTLSQMSHRLEP` `_________________________________________________________________________________________`

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)	159.7
Translation (A)	-17.3
Closure (%)	93.0
Bending Residues ( green )	437 - 446
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

PyMOL Script

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