DynDom - Protein Domain Motions

Pyruvate,orthophosphate Dikinase

(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	Pyruvate,orthophosphate Dikinase
Conformer 1 (PDB)	1vbg (A)
Conformer 2 (PDB)	2r82 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	686	2.41	5 - 367 377 - 379 523 - 583 599 - 636 647 - 874
2	141	1.42	368 - 376 380 - 512
3	24	1.24	584 - 598 638 - 646

Sequence

`________________________________________________________________________________________________________________________` `1vbg(A) : KKRVFHFGKGKSEGNKTMKELLGGKGANLAEMASIGLSVPPGFTVSTEACQQYQDAGCALPAGLWAEIVDGLQWVEEYMGATLGDPQRPLLLSVRSGAAVSMPGMMDTVLNLGLNDEVAA` `:` `2r82(A) : AKWVYKF----EEGNASMRNLLGGKGCNLAEMTILGMPIPQGFTVTTEACTEYYNSGKQITQEIQDQIFEAITWLEELNGKKFGDTEDPLLVSVRSGARASMPGMMDTILNLGLNDVAVE` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1vbg(A) : GLAAKSGE-RFAYDSFRRFLDMFGNVVMDIPRSLFEEKLEHMKESKGLKNDTDLTASDLKELVGQYKEVYLSA-KGEPFPSDPKKQLELAVLAVFNSWESPRAKKYRSINQITGLRGTAV` `:` `2r82(A) : GFAKKTGNPRFAYDSYRRFIQMYSDVVMEVPKSHFEKIIDAMKEEKGVHFDTDLTADDLKELAEKFKAVYKEAMNGEEFPQEPKDQLMGAVKAVFRSWDNPEAIVYRRMNDIPGDWGTAV` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1vbg(A) : NVQCMVFGNMGNTSGTGVLFTRNPNTGEKKLYGEFLVNAQGEDVVAGIRTPEDLDAMKNLMPQAYDELVENCNILESHYKEMQDIEFTVQENRLWMLQCRTGKRTGKSAVKIAVDMVNEG` `:` `2r82(A) : NVQTMVFGNKGETSGTGVAFTRNPDTGEKGIYGRYLINAQGEDVVAGVRTPQPITQLENDMPDCYKQFMDLAMKLEKHFRDMQDMEFTIEEGKLYFLQTRNGKRTAPAALQIACDLVDEG` `________________________________________________________________________________________________________________________` `____367______376________________________________________________________________________________________________________` `1vbg(A) : LVEPRSAIKMVEPGHLDQLLHPQFENPSAYK-DQVIATGLPASPGAAVGQVVFTAEDAEAWHSQGKAAILVRAETSPEDVGGMHAAVGILTERGGMTSHAAVVARGWGKCCVSGCSGIRV` `:` `2r82(A) : MITEEEAVVRIEAKSLDQLLHPTF-NPAALKAGEVIGSALPASPGAAAGKVYFTADEAKAAHEKGERVILVRLETSPEDIEGMHAAEGILTVRGGMTSHAAVVARGMGTCCVSGCGEIKI` `____364______373________________________________________________________________________________________________________` `______________________________512____________________________________________________________________583____________598_` `1vbg(A) : NDAEKLVTIGGHVLREGEWLSLNGSTGEVILGKQPLSPPALSGDLGTFMAWVDDVRKLKVLANADTPDDALTARNNGAQGIGLCRTEHMFFASDERIKAVRQMIMAPTLELRQQALDRLL` `:` `2r82(A) : NEEAKTFELGGHTFAEGDYISLDGSTGKIYKGDIETQEASVSGSFERIMVWADKFRTLKVRTNADTPEDTLNAVKLGAEGIGLCRTEHMFFEAD-RIMKIRKMILSDSVEAREEALNELI` `______________________________509____________________________________________________________________579____________594_` `_____________________________631___________645__________________________________________________________________________` `1vbg(A) : PYQRSDFEGIFRAMDGLPVTIRLLDPPLHEFLPEGNIEDIVSELCAETGANQEDALARIEKLSEVNPMLGFRGCRLGISYPELTEMQARAIFEAAIAMTNQ-GVQVFPEIMVPLVGTPQE` `:` `2r82(A) : PFQKGDFKAMYKALEGRPMTVRYLDPPLHEFVP--HTEEEQAELAKNMGLTLAEVKAKVDELHEFNPMMGHRGCRLAVTYPEIAKMQTRAVMEAAIEVKEETGIDIVPEIMIPLVGEKKE` `_____________________________627___________639__________________________________________________________________________` `________________________________________________________________________________________________________________________` `1vbg(A) : LGHQVTLIRQVAEKVFANVGKTIGYKVGTMIEIPRAALVADEIAEQAEFFSFGTNDLTQMTFGYSRDDVGKFIPVYLAQGILQHDPFEVLDQRGVGELVKFATERGRKARPNLKVGICGE` `:` `2r82(A) : LKFVKDVVVEVAEQVKKEKGSDMQYHIGTMIEIPRAALTADAIAEEAEFFSFGTNDLTQMTFGFSRDDAGKFLDSYYKAKIYESDPFARLDQTGVGQLVEMAVKKGRQTRPGLKCGICGE` `________________________________________________________________________________________________________________________` `________________________________________` `1vbg(A) : HGGEPSSVAFFAKAGLDYVSCSPFRVPIARLAAAQVLV**` `:` `2r82(A) : HGGDPSSVEFCHKVGLNYVSCSPFRVPIARLAAAQAALNN` `________________________________________`

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)	25.1
Translation (A)	-1.1
Closure (%)	14.6
Bending Residues ( green )	367 - 368 376 - 377 379 - 380 512 - 523
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	27.8
Translation (A)	-0.1
Closure (%)	87.6
Bending Residues ( green )	583 - 584 598 - 599 631 - 638 645 - 647
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Hinge

Conformer 1 Contact:
Residue 1 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 1

Movement classification: Shear

PyMOL Script

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