DynDom - Protein Domain Motions

Glutamate--Trna 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	Glutamate--Trna Ligase
Conformer 1 (PDB)	8vc5 (A)
Conformer 2 (PDB)	8vc5 (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	395	0.7	4 - 87 94 - 99 157 - 182 203 - 491
2	83	1.04	88 - 93 100 - 156 183 - 202

Sequence

`________________________________________________________________________________82_________93___98______________________` `8vc5(A) : MTTVRTRIAPSPTGDPHVGTAYIALFNLCFARQHGGQFILRIEDTDQLRSTRESEQQIYDALRWLGIEWDEGPDVGGPHGPYRQSERGHIYKKYSDELVEKGHAFTCFCTPERLDAVRAE` `:` `8vc5(B) : *TTVRTRIAPSPTGDPHVGTAYIALFNLCFARQHGGQFILRIED-----sTRESEQQIYDALRWLGIEWDEGPDVGGPHGPYRQSERGHIYKKYSDELVEKGHAFTCFCTPERLDAVRAE` `________________________________________________________________________________82_________93___98______________________` `_________________________________156_____________________180___________________202______________________________________` `8vc5(A) : QMARKETPRYDGHCMHLPKDEVQRRLAAGESHVTRMKVPTEGVCVVPDMLRGDVEIPWDRMDMQVLMKADGLPTYFLANVVDDHLMGITHVLRGEEWLPSAPKLIKLYEYFGWEQPQLCY` `:` `8vc5(B) : QMARKETPRYDGHCMHLPKDEVQRRLAAGESHVTRMKVPTEGVCVVPDMLRGDVEIPWDRMDMQVLMKADGLPTYFLANVVDDHLMGITHVLRGEEWLPSAPKLIKLYEYFGWEQPQLCY` `_________________________________156_____________________180___________________202______________________________________` `________________________________________________________________________________________________________________________` `8vc5(A) : MPLLRNPDKSKLSKRKNPTSITFYERMGYLPQALLNYLGRMGWSeKFTLAEMIEHFDLSRVSLGGPIFDLEKLSWLNGQWIREQSVEEFAREVQKWALNPEYLMKIAPHVQGRVENFSQI` `:` `8vc5(B) : MPLLRNPDKSKLSKRKNPTSITFYERMGYLPQALLNYLGRMGWSeKFTLAEMIEHFDLSRVSLGGPIFDLEKLSWLNGQWIREQSVEEFAREVQKWALNPEYLMKIAPHVQGRVENFSQI` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `8vc5(A) : APLAGFFFSGGVPLDASLFEHKKLDPTQVRQVLQLVLWKLESLRQWEKERITGCIQAVAEHLQLKLRDVMPLMFPAITGHASSVSVLDAMEILGADLSRYRLRQALELLGGASKKETKEW` `:` `8vc5(B) : APLAGFFFSGGVPLDASLFEHKKLDPTQVRQVLQLVLWKLESLRQWEKERITGCIQAVAEHLQLKLRDVMPLMFPAITGHASSVSVLDAMEILGADLSRYRLRQALELLGGASKKETKEW` `________________________________________________________________________________________________________________________` `________` `8vc5(A) : EKIRDAIP` `:` `8vc5(B) : EKIRDAIP` `________`

Morph

Jmol._Canvas2D (Jmol) "jmolApplet"[x]

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)	9.8
Translation (A)	0.1
Closure (%)	94.1
Bending Residues ( green )	82 - 90 93 - 94 98 - 100 156 - 159 180 - 183 202 - 203
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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