DynDom - Protein Domain Motions

Pyruvate Decarboxylase (Pdc) (E.C.4.1.1.1)

(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 Decarboxylase (Pdc) (E.C.4.1.1.1)
Conformer 1 (PDB)	1pvd (B)
Conformer 2 (PDB)	1qpb (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	411	0.77	4 - 190 217 - 221 243 - 252 254 - 257 260 - 261 275 - 277 290 - 303 351 - 554
2	122	1.09	191 - 216 222 - 242 253 - 253 258 - 259 262 - 274 278 - 289 304 - 350

Sequence

`________________________________________________________________________________________________________________________` `1pvd(B) : SEITLGKYLFERLKQVNVNTVFGLPGDFNLSLLDKIYEVEGMRWAGNANELNAAYAADGYARIKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSIS--------hHTLGNGD` `:` `1qpb(A) : SEITLGKYLFERLKQVNVNTVFGLPGDFNLSLLDKIYEVEGMRWAGNANELNAAYAADGYARIKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSISAQAKQLLLHHTLGNGD` `________________________________________________________________________________________________________________________` `__________________________________________________________________190_______________________216__221__________________24` `1pvd(B) : FTVFHRMSANISETTAMITDIATAPAEIDRCIRTTYVTQRPVYLGLPANLVDLNVPAKLLQTPIDMSLKPNDAESEKEVIDTILALVKDAKNPVILADACCSRHDVKAETKKLIDLTQFP` `:` `1qpb(A) : FTVFHRMSANISETTAMITDIATAPAEIDRCIRTTYVTQRPVYLGLPANLVDLNVPAKLLQTPIDMSLKPNDAESEKEVIDTILVLIKDAKNPVILADACCSRHDVKAETKKLIDLTQFP` `__________________________________________________________________190_______________________216__221__________________24` `2_______252___________________274__________287____________________________________________________________350___________` `1pvd(B) : AFVTPMGKGSISEQHPRYGGVYVGTLSKPEVKEAVESADLILSVGALLSD----------kTKNIVEFHSDHMKIRNATFPGVQMKFVLQKLLTNIADAAKGYKPVAVPARTPANAAVPA` `:` `1qpb(A) : AFVTPMGKGSIDEQHPRYGGVYVGTLSKPEVKEAVESADLILSVGALLSDFNTGSFSYSYKTKNIVEFHSDHMKIRNATFPGVQMKFVLQKLLTAIADAAKGYKPVAVPARTPANAAVPA` `2_______252___________________274__________287____________________________________________________________350___________` `________________________________________________________________________________________________________________________` `1pvd(B) : STPLKQEWMWNQLGNFLQEGDVVIAETGTSAFGINQTTFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIEKLIH` `:` `1qpb(A) : STPLKQEWMWNQLGNFLQEGDVVIAETGTSAFGINQTTFPNNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYLFVLNNDGYTIEKLIH` `________________________________________________________________________________________________________________________` `___________________________________________________________________________` `1pvd(B) : GPKAQYNEIQGWDHLSLLPTFGAKDYETHRVATTGEWDKLTQDKSFNDNSKIRMIEIMLPVFDAPQNLVKQAKLT` `:` `1qpb(A) : GPKAQYNEIQGWDHLSLLPTFGAKDYETHRVATTGEWDKLTQDKSFNDNSKIRMIEVMLPVFDAPQNLVEQAKLT` `___________________________________________________________________________`

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)	11.8
Translation (A)	-0.9
Closure (%)	97.8
Bending Residues ( green )	190 - 191 216 - 217 221 - 222 242 - 243 252 - 262 274 - 275 277 - 278 287 - 304 350 - 351
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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