DynDom - Protein Domain Motions

Abc Transporter, Substrate Binding Protein (Amino Acid)

(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	Abc Transporter, Substrate Binding Protein (Amino Acid)
Conformer 1 (PDB)	3ip5 (A)
Conformer 2 (PDB)	3ipc (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	242	0.23	3 - 124 129 - 140 215 - 218 220 - 228 239 - 333
2	97	0.44	125 - 128 141 - 214 219 - 219 229 - 233 334 - 346

Sequence

`________________________________________________________________________________________________________________________` `3ip5(A) : MDVVIAVGAPLTGPNAAFGAQIQKGAEQAAKDINAAGGINGEQIKIVLGDDVSDPKQGISVANKFVADGVKFVVGHFNSGVSIPASEVYAENGILEITPAATNPVFTERGLWNTFRTCGR` `:` `3ipc(A) : MDVVIAVGAPLTGPNAAFGAQIQKGAEQAAKDINAAGGINGEQIKIVLGDDVSDPKQGISVANKFVADGVKFVVGHANSGVSIPASEVYAENGILEITPAATNPVFTERGLWNTFRTCGR` `________________________________________________________________________________________________________________________` `_124_128_________140_______________________________________________________________________214_218_______228__233_______` `3ip5(A) : DDQQGGIAGKYLADHFKDAKVAIIHDKTPYGQGLADETKKAANAAGVTEVMYEGVNVGDKDFSALISKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKAKLVSGDGIVSNELASIAGDA` `:` `3ipc(A) : DDQQGGIAGKYLADHFKDAKVAIIHDKTPYGQGLADETKKAANAAGVTEVMYEGVNVGDKDFSALISKMKEAGVSIIYWGGLHTEAGLIIRQAADQGLKAKLVSGDGIVSNELASIAGDA` `_124_128_________140_______________________________________________________________________214_218_______228__233_______` `__________________________________________________________________________________________333_______________` `3ip5(A) : VEGTLNTFGPDPTLRPENKELVEKFKAAGFNPEAYTLYSYAAMQAIAGAAKAAGSVEPEKVAEALKKGSFPTALGEISFDEKGDPKLPGYVMYEWKKGPDGKFTYIQQ` `:` `3ipc(A) : VEGTLNTFGPDPTLRPENKELVEKFKAAGFNPEAYTLYSYAAMQAIAGAAKAAGSVEPEKVAEALKKGSFPTALGEISFDEKGDPKLPGYVMYEWKKGPDGKFTYIQQ` `__________________________________________________________________________________________333_______________`

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)	2.5
Translation (A)	-0.2
Closure (%)	79.7
Bending Residues ( green )	124 - 125 128 - 129 140 - 141 214 - 216 218 - 220 228 - 229 233 - 241 333 - 334
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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