DynDom - Protein Domain Motions

Pyruvate Phosphate 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 Phosphate Dikinase
Conformer 1 (PDB)	1kbl (A)
Conformer 2 (PDB)	1vbg (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	483	2.19	242 - 278 284 - 378 518 - 869
2	241	2.47	4 - 241 279 - 283
3	138	1.74	379 - 517

Sequence

`________________________________________________________________________________________________________________________` `1kbl(A) : AKWVYKF----EEGNASMRNLLGGKGCNLAEMTILGMPIPQGFTVTTEACTEYYNSGKQITQEIQDQIFEAITWLEELNGKKFGDTEDPLLVSVRSGARASMPGMMDTILNLGLNDVAVE` `:` `1vbg(A) : KKRVFHFGKGKSEGNKTMKELLGGKGANLAEMASIGLSVPPGFTVSTEACQQYQDAGCALPAGLWAEIVDGLQWVEEYMGATLGDPQRPLLLSVRSGAAVSMPGMMDTVLNLGLNDEVAA` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1kbl(A) : GFAKKTGNPRFAYDSYRRFIQMYSDVVMEVPKSHFEKIIDAMKEEKGVHFDTDLTADDLKELAEKFKAVYKEAMNGEEFPQEPKDQLMGAVKAVFRSWDNPRAIVYRRMNDIPGDWGTAV` `:` `1vbg(A) : GLAAKSGE-RFAYDSFRRFLDMFGNVVMDIPRSLFEEKLEHMKESKGLKNDTDLTASDLKELVGQYKEVYLSA-KGEPFPSDPKKQLELAVLAVFNSWESPRAKKYRSINQITGLRGTAV` `________________________________________________________________________________________________________________________` `_241________________________________276_________________________________________________________________________________` `1kbl(A) : NVQTMVFGNKGETSGTGVAFTRNPSTGEKGIYGEYLINAQGEDVVAGVRTPQPITQLENDMPDCYKQFMDLAMKLEKHFRDMQDMEFTIEEGKLYFLQTRNGKRTAPAALQIACDLVDEG` `:` `1vbg(A) : NVQCMVFGNMGNTSGTGVLFTRNPNTGEKKLYGEFLVNAQGEDVVAGIRTPEDLDAMKNLMPQAYDELVENCNILESHYKEMQDIEFTVQENRLWMLQCRTGKRTGKSAVKIAVDMVNEG` `_244________________________________279_________________________________________________________________________________` `__________________378___________________________________________________________________________________________________` `1kbl(A) : MITEEEAVVRIEAKSLDQLLHPTF-NPAALKAGEVIGSALPASPGAAAGKVYFTADEAKAAHEKGERVILVRLETSPEDIEGMHAAEGILTVRGGMTSHAAVVARGMGTCCVSGCGEIKI` `:` `1vbg(A) : LVEPRSAIKMVEPGHLDQLLHPQFENPSAYK-DQVIATGLPASPGAAVGQVVFTAEDAEAWHSQGKAAILVRAETSPEDVGGMHAAVGILTERGGMTSHAAVVARGWGKCCVSGCSGIRV` `__________________381___________________________________________________________________________________________________` `__________________________________513___________________________________________________________________________________` `1kbl(A) : NEEAKTFELGGHTFAEGDYISLDGSTGKIYKGDIETQEASVSGSFERIMVWADKFRTLKVRTNADTPEDTLNAVKLGAEGIGLCRTEHMFFEAD-RIMKIRKMILSDSVEAREEALNELI` `:` `1vbg(A) : NDAEKLVTIGGHVLREGEWLSLNGSTGEVILGKQPLSPPALSGDLGTFMAWVDDVRKLKVLANADTPDDALTARNNGAQGIGLCRTEHMFFASDERIKAVRQMIMAPTLELRQQALDRLL` `__________________________________516___________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1kbl(A) : PFQKGDFKAMYKALEGRPMTVRYLDPPLHEFVP--HTEEEQAELAKNMGLTLAEVKAKVDELHEFNPMMGHRGCRLAVTYPEIAKMQTRAVMEAAIEVKEETGIDIVPEIMIPLVGEKKE` `:` `1vbg(A) : PYQRSDFEGIFRAMDGLPVTIRLLDPPLHEFLPEGNIEDIVSELCAETGANQEDALARIEKLSEVNPMLGFRGCRLGISYPELTEMQARAIFEAAIAMTNQ-GVQVFPEIMVPLVGTPQE` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1kbl(A) : LKFVKDVVVEVAEQVKKEKGSDMQYHIGTMIEIPRAALTADAIAEEAEFFSFGTNDLTQMTFGFSRDDAGKFLDSYYKAKIYESDPFARLDQTGVGQLVEMAVKKGRQTRPGLKCGICGE` `:` `1vbg(A) : LGHQVTLIRQVAEKVFANVGKTIGYKVGTMIEIPRAALVADEIAEQAEFFSFGTNDLTQMTFGYSRDDVGKFIPVYLAQGILQHDPFEVLDQRGVGELVKFATERGRKARPNLKVGICGE` `________________________________________________________________________________________________________________________` `________________________________________` `1kbl(A) : HGGDPSSVEFCHKVGLNYVSCSPFRVPIARLAAAQAALNN` `:` `1vbg(A) : HGGEPSSVAFFAKAGLDYVSCSPFRVPIARLAAAQVLV**` `________________________________________`

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)	40.2
Translation (A)	0.3
Closure (%)	56.4
Bending Residues ( green )	241 - 242 276 - 289
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	90.8
Translation (A)	0.1
Closure (%)	34.8
Bending Residues ( green )	378 - 379 513 - 520
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: Hinge

PyMOL Script

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