DynDom - Protein Domain Motions

Nad-Specific Glutamate Dehydrogenase

(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	Nad-Specific Glutamate Dehydrogenase
Conformer 1 (PDB)	7jsr (A)
Conformer 2 (PDB)	7jsr (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	1159	0.26	370 - 1586
2	289	0.66	47 - 369

Sequence

`________________________________________________________________________________________________________________________` `7jsr(A) : TGPLAVAAHDDLVSDDLVAAHYRLASrAPGETKAAVYPGDAGSGAALQIVTDQAPlVDSVTVLLHRHGIAYTAInPVFRVgADECWILVPITAAADGEALTEATRLVPGILAEARQIGLD` `:` `7jsr(B) : *******************AHYRLASrAPGETKAAVYPGDAGSGAALQIVTDQAPlVDSVTVLLHRHGIAYTAInPVFRVgADECWILVPITAAADGEALTEATRLVPGILAEARQIGLD` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `7jsr(A) : SGAiAALHGLANDLATDLEGHFPNAERKEVAALLRWLADGHFVLLGYQQCVVGDGNAEVDPASRLGVLRLRNDVLPPLTDSDDLLVLAQATpSYLRYGAYPYIVVVRESPGASRVIEHRF` `:` `7jsr(B) : SGAiAALHGLANDLATDLEGHFPNAERKEVAALLRWLADGHFVLLGYQQCVVGDGNAEVDPASRLGVLRLRNDVLPPLTDSDDLLVLAQATpSYLRYGAYPYIVVVRESPGASRVIEHRF` `________________________________________________________________________________________________________________________` `__________________________________________________________354___________________________________________________________` `7jsr(A) : VGLFTVAAnANALEIPLISRRVEEALAaHRDPSHPGQLLRDIIQTIPRPELFALSSKQLLEaLAVVDLtLLFLRADHhFVSCLVYLPRDRYTTAVRLEqDILVRELGGAGIDYSARVSES` `:` `7jsr(B) : VGLFTVAAnANALEIPLISRRVEEALAaHRDPSHPGQLLRDIIQTIPRPELFALSSKQLLEaLAVVDLtLLFLRADHhFVSCLVYLPRDRYTTAVRLEqDILVRELGGAGIDYSARVSES` `__________________________________________________________354___________________________________________________________` `________________________________________________________________________________________________________________________` `7jsr(A) : PWAVVHFTVRLnESRIQDLLTEATRNWGDRiSAAAAASISPAALEHYAHAFPEDYKQAFAPQDAIADISLIEALQDDSVKLVLADTAEDRVWKLTWYLGGHSASLSELLPlQSgVVVLEE` `:` `7jsr(B) : PWAVVHFTVRLnESRIQDLLTEATRNWGDRiSAAAAASISPAALEHYAHAFPEDYKQAFAPQDAIADISLIEALQDDSVKLVLADTAEDRVWKLTWYLGGHSASLSELLPlQSgVVVLEE` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `7jsr(A) : RPFTLRRTDGLPVWIYQFKISPHPSIPHAPDAEAQRDTAQRFADAVTAIWHGRVEIDRFNELVrAGLTWQQVVVLRAYAKYLRQAGFPYSQSHIESVLNENPHTTRSLIDLFEALFDPSQ` `:` `7jsr(B) : RPFTLRRTDGLPVWIYQFKISPHPSIPHAPDAEAQRDTAQRFADAVTAIWHGRVEIDRFNELVrAGLTWQQVVVLRAYAKYLRQAGFPYSQSHIESVLNENPHTTRSLIDLFEALFDPSQ` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `7jsr(A) : ETDGRRDAQGAAAAVAADIDALVSLDTDRVLRAFANLIEATLRTNYFVrNVLAFKLNPLVIKELPLPRPKFEIFVYSPRVEGVHLRFGFVARGGLRWSDRREDFRTEILGLVKAQAVKNA` `:` `7jsr(B) : ETDGRRDAQGAAAAVAADIDALVSLDTDRVLRAFANLIEATLRTNYFVrNVLAFKLNPLVIKELPLPRPKFEIFVYSPRVEGVHLRFGFVARGGLRWSDRREDFRTEILGLVKAQAVKNA` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `7jsr(A) : VIVPVGAKGGFVVKRPPTLTGDAAADREATRAEGVECYRLFISGLLDVTDNVDKATGAVVTPPEVVRRDGEDAYLVVAADKGTATFSDIANEVAKSYGFWLGDAFAgITAKGAWESVKRH` `:` `7jsr(B) : VIVPVGAKGGFVVKRPPTLTGDAAADREATRAEGVECYRLFISGLLDVTDNVDKATGAVVTPPEVVRRDGEDAYLVVAADKGTATFSDIANEVAKSYGFWLGDAFAgITAKGAWESVKRH` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `7jsr(A) : FREgVDTQTQDFTVVGIGDsGDVFGNGlLSKHIRLVAAFDHRDIFLDPNPDAGRSWDERKRLFDLPRSSWADYDKSLISEGGGVYSRQQKSIPISPQVRTALGLDADVEELTPPALIKAI` `:` `7jsr(B) : FREgVDTQTQDFTVVGIGDsGDVFGNGlLSKHIRLVAAFDHRDIFLDPNPDAGRSWDERKRLFDLPRSSWADYDKSLISEGGGVYSRQQKSIPISPQVRTALGLDADVEELTPPALIKAI` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `7jsr(A) : LKAPVDLLWNGGIGTYIKAETEADADnDQIRVCGNQVRAKVIGEGGNLGVTALGRIEFDLAGGRINTDALDNSAGVDCSDHEVNIKILIDSAVTAGKVTPEERTELLLStDEVGELVLAD` `:` `7jsr(B) : LKAPVDLLWNGGIGTYIKAETEADADnDQIRVCGNQVRAKVIGEGGNLGVTALGRIEFDLAGGRINTDALDNSAGVDCSDHEVNIKILIDSAVTAGKVTPEERTELLLStDEVGELVLAD` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `7jsr(A) : NRDQNDLgTSRANAASLLSVHARiKDLVDNRGLNRELEALPSEKEIRRRADAGIGLTSPELATLaHVKLALKDDVLASDLPDQEVFASRLPYYFPTRLREELHGEIRSHQLRREIITTlV` `:` `7jsr(B) : NRDQNDLgTSRANAASLLSVHARiKDLVDNRGLNRELEALPSEKEIRRRADAGIGLTSPELATLaHVKLALKDDVLASDLPDQEVFASRLPYYFPTRLREELHGEIRSHQLRREIITTlV` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `7jsr(A) : NDLVDTAGISYAYRITEDVGVGPVDAVRSYVAINAIFGIGDVWRRIRAAGDAGVPTSVTDRtLDLRRLVDRAGRWLLNYRPQPLAVGAEINRFGAKVAALTPRsEWLRGDDKAIVSKEAG` `:` `7jsr(B) : NDLVDTAGISYAYRITEDVGVGPVDAVRSYVAINAIFGIGDVWRRIRAAGDAGVPTSVTDRtLDLRRLVDRAGRWLLNYRPQPLAVGAEINRFGAKVAALTPRsEWLRGDDKAIVSKEAG` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `7jsr(A) : DFASHGVPEDLAYHIATGLYQYSLLDVIDIADIVDREPDEVADTYFALdHLGADALLTAVSRLSRDDRWHSLARLAIRDDIYGSLRALCFDVLAVGEPDENGEEKIAEWETTNSSRVTRA` `:` `7jsr(B) : DFASHGVPEDLAYHIATGLYQYSLLDVIDIADIVDREPDEVADTYFALdHLGADALLTAVSRLSRDDRWHSLARLAIRDDIYGSLRALCFDVLAVGEPDENGEEKIAEWETTNSSRVTRA` `________________________________________________________________________________________________________________________` `_______________________________` `7jsr(A) : RRTLTEIYKDGEQDLATLSVAARQIRStRTS` `:` `7jsr(B) : RRTLTEIYKDGEQDLATLSVAARQIRStRTS` `_______________________________`

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	38.1
Translation (A)	4.0
Closure (%)	4.0
Bending Residues ( green )	354 - 381
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

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