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)	1vbh (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	745	0.63	5 - 390 395 - 395 401 - 404 470 - 470 501 - 501 508 - 508 512 - 514 518 - 874
2	113	0.57	391 - 394 396 - 400 405 - 469 471 - 500 502 - 507 509 - 511 515 - 517

Sequence

`________________________________________________________________________________________________________________________` `1vbg(A) : KKRVFHFGKGKSEGNKTMKELLGGKGANLAEMASIGLSVPPGFTVSTEACQQYQDAGCALPAGLWAEIVDGLQWVEEYMGATLGDPQRPLLLSVRSGAAVSMPGMMDTVLNLGLNDEVAA` `:` `1vbh(A) : KKRVFHFGKGKSEGNKTMKELLGGKGANLAEMASIGLSVPPGFTVSTEACQQYQDAGCALPAGLWAEIVDGLQWVEEYMGATLGDPQRPLLLSVRSGAAVSMPGMMDTVLNLGLNDEVAA` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1vbg(A) : GLAAKSGERFAYDSFRRFLDMFGNVVMDIPRSLFEEKLEHMKESKGLKNDTDLTASDLKELVGQYKEVYLSAKGEPFPSDPKKQLELAVLAVFNSWESPRAKKYRSINQITGLRGTAVNV` `:` `1vbh(A) : GLAAKSGERFAYDSFRRFLDMFGNVVMDIPRSLFEEKLEHMKESKGLKNDTDLTASDLKELVGQYKEVYLSAKGEPFPSDPKKQLELAVLAVFNSWESPRAKKYRSINQITGLRGTAVNV` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1vbg(A) : QCMVFGNMGNTSGTGVLFTRNPNTGEKKLYGEFLVNAQGEDVVAGIRTPEDLDAMKNLMPQAYDELVENCNILESHYKEMQDIEFTVQENRLWMLQCRTGKRTGKSAVKIAVDMVNEGLV` `:` `1vbh(A) : QCMVFGNMGNTSGTGVLFTRNPNTGEKKLYGEFLVNA---------rTPEDLDAMKNLMPQAYDELVENCNILESHYKEMQDIEFTVQENRLWMLQCRTGKRTGKSAVKIAVDMVNEGLV` `________________________________________________________________________________________________________________________` `______________________387____394___400_404______________________________________________________________469_____________` `1vbg(A) : EPRSAIKMVEPGHLDQLLHPQFENPSAYKDQVIATGLPASPGAAVGQVVFTAEDAEAWHSQGKAAILVRAETSPEDVGGMHAAVGILTERGGMTSHAAVVARGWGKCCVSGCSGIRVNDA` `:` `1vbh(A) : EPRSAIKMVEPGHLDQLLHPQFENPSAYKDQVIATGLPASPGAAVGQVVFTAEDAEAWHSQGKAAILVRAETSPEDVGGMHAAVGILTE---mTSHAAVVARGWGKCCVSGCSGIRVNDA` `______________________387____394___400_404______________________________________________________________469_____________` `_______________500____507_511___517_____________________________________________________________________________________` `1vbg(A) : EKLVTIGGHVLREGEWLSLNGSTGEVILGKQPLSPPALSGDLGTFMAWVDDVRKLKVLANADTPDDALTARNNGAQGIGLCRTEHMFFASDERIKAVRQMIMAPTLELRQQALDRLLPYQ` `:` `1vbh(A) : EKLVTIGGHVLREGEWLSLNGSTGEVILGKQPLSPPALSGDLGTFMAWVDDVRKLKVLANADTPDDALTARNNGAQGIGLCRTEHMFFASDERIKAVRQMIMAPTLELRQQALDRLLPYQ` `_______________500____507_511___517_____________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1vbg(A) : RSDFEGIFRAMDGLPVTIRLLDPPLHEFLPEGNIEDIVSELCAETGANQEDALARIEKLSEVNPMLGFRGCRLGISYPELTEMQARAIFEAAIAMTNQGVQVFPEIMVPLVGTPQELGHQ` `:` `1vbh(A) : RSDFEGIFRAMDGLPVTIRLLDPPLHEFLPEGNIEDIVSELCAETGANQEDALARIEKLSEVNPMLGFRGCRLGISYPELTEMQARAIFEAAIAMTNQGVQVFPEIMVPLVGTPQELGHQ` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1vbg(A) : VTLIRQVAEKVFANVGKTIGYKVGTMIEIPRAALVADEIAEQAEFFSFGTNDLTQMTFGYSRDDVGKFIPVYLAQGILQHDPFEVLDQRGVGELVKFATERGRKARPNLKVGICGEHGGE` `:` `1vbh(A) : VTLIRQVAEKVFANVGKTIGYKVGTMIEIPRAALVADEIAEQAEFFSFGTNDLTQMTFGYSRDDVGKFIPVYLAQGILQHDPFEVLDQRGVGELVKFATERGRKARPNLKVGICGEHGGE` `________________________________________________________________________________________________________________________` `__________________________________` `1vbg(A) : PSSVAFFAKAGLDYVSCSPFRVPIARLAAAQVLV` `:` `1vbh(A) : PSSVAFFAKAGLDYVSCSPFRVPIARLAAAQVLV` `__________________________________`

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)	4.7
Translation (A)	0.4
Closure (%)	24.9
Bending Residues ( green )	387 - 391 394 - 396 400 - 402 404 - 405 469 - 471 500 - 502 507 - 509 511 - 512 514 - 515 517 - 519
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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