DynDom - Protein Domain Motions

D-3-Phosphoglycerate Dehydrogenase (Phosphoglycerate 3 Dehydrogenase) (E.C.1.1.1.95)

(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	D-3-Phosphoglycerate Dehydrogenase (Phosphoglycerate 3 Dehydrogenase) (E.C.1.1.1.95)
Conformer 1 (PDB)	1sc6 (B)
Conformer 2 (PDB)	1sc6 (D)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	206	0.64	9 - 106 298 - 408
2	162	0.67	107 - 297

Sequence

`_________________________________________________________________________________________________106____________________` `1sc6(B) : EKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLRSRTHLTEDVINAAEKLVAIGAFAIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLLLRG` `:` `1sc6(D) : EKDKIKFLLVEGVHQKALESLRAAGYTNIEFHKGALDDEQLKESIRDAHFIGLRSRTHLTEDVINAAEKLVAIGAFAIGTNQVDLDAAAKRGIPVFNAPFSNTRSVAELVIGELLLLLRG` `_________________________________________________________________________________________________106____________________` `________________________________________________________________________________________________________________________` `1sc6(B) : VPEANAKAHRGVGNsFEARGKKLGIIGYGHIGTQLGILAESLGyVYFYDIENKLPLGNATQVQHLSDLLNsDVVSLHVPENPSTKNgAKEISLkPGSLLINASRGTVVDIPALADALASK` `:` `1sc6(D) : VPEANAKAHRGVG-sFEARGKKLGIIGYGHIGTQLGILAESLGyVYFYDIENKLPLGNATQVQHLSDLLNsDVVSLHVPENPSTKNgAKEISLkPGSLLINASRGTVVDIPALADALASK` `________________________________________________________________________________________________________________________` `______________________291_______________________________________________________________________________________________` `1sc6(B) : HLAGAAID----sPLAEFDNVLLTPHIGGSTQEAQENIGLEVAGKLIKYSDNGSTLSAVNFPEVSLPLHGGRRLhIHENRPGVLTALNKIFAEQGVNIAAQYLQTSAQgYVVIDIEADED` `:` `1sc6(D) : HLAGAAIDVpFTSPLAEFDNVLLTP----sTQEAQENIGLEVAGKLIKYSDNGSTLSAVNFPEVSLPLHGGRRLhIHENRPGVLTALNKIFAEQGVNIAAQYLQTSAQgYVVIDIEADED` `______________________291_______________________________________________________________________________________________` `_____________________` `1sc6(B) : VAEKALQAkAIPGTIRARLLY` `:` `1sc6(D) : VAEKALQAkAIPGTIRARLLY` `_____________________`

Morph

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

jsmol/j2s/core/package.js

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jsmol/j2s/core/core.z.js

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jsmol/j2s/J/g3d/PixelatorT.js

-- required by J.g3d.Graphics3D ajax=false async=true

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	16.5
Translation (A)	-0.2
Closure (%)	93.9
Bending Residues ( green )	106 - 109 291 - 300
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification:

No Contacts

PyMOL Script

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