DynDom - Protein Domain Motions

Udp-N-Acetylmuramate-L-Alanine Ligase

(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	Udp-N-Acetylmuramate-L-Alanine Ligase
Conformer 1 (PDB)	1p3d (A)
Conformer 2 (PDB)	2f00 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	406	1.15	18 - 24 33 - 48 51 - 54 56 - 66 70 - 71 74 - 92 103 - 471
2	25	0.76	25 - 32 49 - 50 55 - 55 67 - 69 72 - 73 93 - 102

Sequence

`_____________________24_____32______________48____54__________66________________________92_______102____________________` `1p3d(A) : ********IIPErRVQQIHFIGIGGAGsGIAEILLNEGYQISGSDIADGVVTQRLAQAGAKIYIGHAEEHIEGASVVVVSSAIKDDNPELVTSKQKRIPVIQRAQlAEIrFRHGIAVA` `:` `2f00(A) : NTQQLAKLRSIVPErRVRHIHFVGIGGAGgGIAEVLANEGYQISGSDLAPNPVTQQL-nLGATIYFNHRPENVRDASVVVVSSAISADNPEIVAAHEARIPVIRRAElAELrFRHGIAIA` `_____________________25_____33______________49____55__________67________________________93_______103____________________` `________________________________________________________________________________________________________________________` `1p3d(A) : GTHGKTTTTAiS-iYTQAKLDPTFVNGGLVKSAGKNAHLGASRYLIAEADESDASFLHLQPvSVVTN-ePDHdTYEGDFEK-kATYVKFLHNLPFYGLAVcADDPVL-eLVPKVGRQVIT` `:` `2f00(A) : GTHGKTTTTAvSSIYAEAGLDPTFVNGGLVKAAGVHARLGHGRYLIAEADESDASFLHLQPvAIVTNIEADHdTYQGDFENLKQTFINFLHNLPFYGRAVcVDDPVIRELLPRVGRQTTT` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1p3d(A) : YGFSEQADYRIEDYEQTGFQGHYTVICPNNERINVLLNVPGKHNALNATAALAVAKEEGIANEAILEALADFQGAGRRFDQLGEF-IRP-NGK--VRLVDDYGHHPTEVGVTIKAAREGW` `:` `2f00(A) : YGFSEDADVRVEDYQQIGPQGHFTLLRQDKEP-rVTLNAPGRHNALNAAAAVAVATEEGIDDEAILRALESFQGTGRRFDFLGEFPLEPVNGKSGTAlVDDYGHHPTEVDATIKAARAGW` `________________________________________________________________________________________________________________________` `_______________________________________________________________________________________________________________` `1p3d(A) : GDKRIViFQPHRYSRTRDLFDDFVQVLSQVDALIlDVYAAGEAPIVGADSKSLCRSIRNLGKVDPILVSDTSQLGDVLDQIIQDGDLILAQGAGSVSKISRGLAESW**` `:` `2f00(A) : PDKNLVlFQPHRFTRTRDLYDDFANVLTQVDTLLlEVYPAGEAPIPGADSRSLCRT-------dPILVPDPARVAE-lAPVLTGNDLILVQGAGNIGKIARSLAEIKLKPQ` `_______________________________________________________________________________________________________________`

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)	8.0
Translation (A)	0.1
Closure (%)	94.3
Bending Residues ( green )	24 - 25 32 - 33 48 - 51 54 - 56 66 - 74 92 - 93 102 - 103
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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