DynDom - Protein Domain Motions

Nad-Dependent Malic Enzyme, Mitochondrial

(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-Dependent Malic Enzyme, Mitochondrial
Conformer 1 (PDB)	1pjl (A)
Conformer 2 (PDB)	1qr6 (A)
Window Length	7
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	432	0.62	90 - 100 121 - 195 197 - 479 485 - 555
2	98	0.83	26 - 89 101 - 120 196 - 196 480 - 484 556 - 569

Sequence

`____________________________________________________________89________100________________120____________________________` `1pjl(A) : EKGKPLlNPRTNKGaFTLQERQlGLQGLLPPKIETQDIQALRFHRNLKKtSPLEKYIYIgIQERNEKLFYRILQDDIESLpIVYTPTVGLACSQYGHIFRRPKGLFISISDRGHVRSIVD` `:` `1qr6(A) : EKGKPLlNPRTNKGaFTLQERQlGLQGLLPPKIETQDIQALRFHRNLKKtSPLEKYIYIgIQERNEKLFYRILQDDIESLpIVYTPTVGLACSQYGHIFRRPKGLFISISDRGHVRSIVD` `____________________________________________________________89________100________________120____________________________` `___________________________________________195__________________________________________________________________________` `1pjl(A) : NWPENHVKAVVVTDGERILGLGDLGVYGgIPVGKLCLYTACAGIRPDRCLPVCIDVGTDNIALLKDPFYgLYQKRDRTQQYDDLIDEFkAITDRYGRNTLIQFEDFGNHNAFRFLRKYRE` `:` `1qr6(A) : NWPENHVKAVVVTDGERILGLGDLGVYGgIPVGKLCLYTACAGIRPDRCLPVCIDVGTDNIALLKDPFYgLYQKRDRTQQYDDLIDEFkAITDRYGRNTLIQFEDFGNHNAFRFLRKYRE` `___________________________________________195__________________________________________________________________________` `________________________________________________________________________________________________________________________` `1pjl(A) : KYCTFNDDIQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIANLIVsvENGLSEQEAQKKIWfDKYGLLVKGRKAKIDSYQEPFTHSAPESIPDTFEDAVNILKPSTIIGVAG` `:` `1qr6(A) : KYCTFNDDIQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIANLIVsvENGLSEQEAQKKIWfDKYGLLVKGRKAKIDSYQEPFTHSAPESIPDTFEDAVNILKPSTIIGVAG` `________________________________________________________________________________________________________________________` `_________________________________________________________________________________479__484_______________________________` `1pjl(A) : AGRLFTPDVIRAaSINERPVIFALSNPTAQAECTAEEAYTLTEGRCLFASGSPFGPVKLTDGRVFTPGQGNNVYIFPGVALAVILCNTRHISDSVFLEAAKALTSQLTDEELAQGRLYPP` `:` `1qr6(A) : AGRLFTPDVIRAaSINERPVIFALSNPTAQAECTAEEAYTLTEGRCLFASGSPFGPVKLTDGRVFTPGQGNNVYIFPGVALAVILCNTRHISDSVFLEAAKALTSQLTDEELAQGRLYPP` `_________________________________________________________________________________479__484_______________________________` `____________________________________555__________________` `1pjl(A) : LANIQEVSINIAIKVTEYLYANKaFRYPEPEDKAKYVKERTWRSEYDSLLPDVYEWP` `:` `1qr6(A) : LANIQEVSINIAIKVTEYLYANKaFRYPEPEDKAKYVKERTWRSEYDSLLPDVYEWP` `____________________________________555__________________`

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)	5.6
Translation (A)	0.3
Closure (%)	99.9
Bending Residues ( green )	89 - 90 100 - 101 120 - 121 195 - 197 479 - 480 484 - 485 555 - 556
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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