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)	1qr6 (A)
Conformer 2 (PDB)	1efk (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	255	0.56	88 - 98 100 - 104 119 - 287 467 - 492 496 - 498 514 - 515 518 - 560
2	74	0.79	25 - 87 99 - 99 105 - 110 516 - 517 561 - 568
3	190	0.56	288 - 463 493 - 495 499 - 513

Sequence

`____________________________________________________________87_________98___104__110____________________________________` `1qr6(A) : **EKGKPLlNPRTNKGaFTLQERQlGLQGLLPPKIETQDIQALRFHRNLKKtSPLEKYIYIgIQERNEKLFYRILQDDIESLpIVYTPTVGLACSQYGHIFRRPKGLFISISDRGHVRSI` `:` `1efk(A) : IKEKGKPLlNPRTNKGaFTLQERQlGLQGLLPPKIETQDIQALRFHRNLKKtSPLEKYIYIgIQERNEKLFYRILQDDIESLpIVYTPTVGLACSQYGHIFRRPKGLFISISDRGHVRSI` `____________________________________________________________87_________98___104__110____________________________________` `________________________________________________________________________________________________________________________` `1qr6(A) : VDNWPENHVKAVVVTDGERILGLGDLGVYGgIPVGKLCLYTACAGIRPDRCLPVCIDVGTDNIALLKDPFYgLYQKRDRTQQYDDLIDEFkAITDRYGRNTLIQFEDFGNHNAFRFLRKY` `:` `1efk(A) : VDNWPENHVKAVVVTDGERILGLGDLGVYGgIPVGKLCLYTACAGIRPDRCLPVCIDVGTDNIALLKDPFYgLYQKRDRTQQYDDLIDEFkAITDRYGRNTLIQFEDFGNHNAFRFLRKY` `________________________________________________________________________________________________________________________` `_______________287______________________________________________________________________________________________________` `1qr6(A) : REKYCTFNDDIQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIANLIVsvENGLSEQEAQKKIWfDKYGLLVKGRKAKIDSYQEPFTHSAPESIPDTFEDAVNILKPSTIIGV` `:` `1efk(A) : REKYCTFNDDIQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIANLIVsvENGLSEQEAQKKIWfDKYGLLVKGRKAKIDSYQEPFTHSAPESIPDTFEDAVNILKPSTIIGV` `_______________287______________________________________________________________________________________________________` `___________________________________________________________________463__________________________492___498______________5` `1qr6(A) : AGAGRLFTPDVIRAaSINERPVIFALSNPTAQAECTAEEAYTLTEGRCLFASGSPFGPVKLTDGRVFTPGQGNNVYIFPGVALAVILCNTRHISDSVFLEAAKALTSQLTDEELAQGRLY` `:` `1efk(A) : AGAGRLFTPDVIRAaSINERPVIFALSNPTAQAECTAEEAYTLTEGRCLFASGSPFGPVKLTDGRVFTPGQGNNVYIFPGVALAVILCNTRHISDSVFLEAAKALTSQLTDEELAQGRLY` `___________________________________________________________________463__________________________492___498______________5` `15_________________________________________560_____________` `1qr6(A) : PPLANIQEVSINIAIKVTEYLYANKaFRYPEPEDKAKYVKERTWRSEYDSLLPDVYEWP` `:` `1efk(A) : PPLANIQEVSINIAIKVTEYLYANKaFRYPEPEDKAKYVKERTWRSEYDSLLPDVYEWP` `15_________________________________________560_____________`

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)	6.3
Translation (A)	0.3
Closure (%)	99.1
Bending Residues ( green )	87 - 88 98 - 101 104 - 106 110 - 122 515 - 518 560 - 561
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	10.8
Translation (A)	-0.1
Closure (%)	94.7
Bending Residues ( green )	287 - 288 463 - 469 492 - 493 495 - 496 498 - 499 513 - 514
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: Hinge

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