DynDom - Protein Domain Motions

Penicillin-Binding Protein 2X

(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	Penicillin-Binding Protein 2X
Conformer 1 (PDB)	1rp5 (A)
Conformer 2 (PDB)	1rp5 (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	59	0.5	67 - 78 89 - 92 94 - 94 182 - 185 197 - 197 216 - 222 228 - 228 230 - 257 304 - 304
2	528	0.38	79 - 88 186 - 196 198 - 215 223 - 227 229 - 229 258 - 303 305 - 748
3	88	0.32	93 - 93 95 - 181

Sequence

`_____________78________88__92______________________________________________________________________________________181_1` `1rp5(A) : KVHQTTRTVPAKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELETAEVKGIDFTTS` `:` `1rp5(B) : KVHQTTRTVPAKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELETAEVKGIDFTTS` `_____________78________88__92______________________________________________________________________________________181_1` `85________196________________215____222__227___________________________257___________________________________________303` `1rp5(A) : PNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDGIITYEKDRLGNIVPGTEQVSQQTVDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILA` `:` `1rp5(B) : PNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDGIITYEKDRLGNIVPGTEQVSQQTVDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILA` `85________196________________215____222__227___________________________257___________________________________________303` `________________________________________________________________________________________________________________________` `1rp5(A) : TTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVNEGLTGGRMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGV` `:` `1rp5(B) : TTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDV-------rMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGV` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1rp5(A) : PTRFGLTDEYAGQLPADNIVNIAMSAFGQGISVTQTQMLRAFTAIANDGVMLEPKFISALYDPNDQSVRKSQKEIVGNPVSKEAASVTRDHMVMVGTDPTYGTMYNHSTGKATVNVPGQN` `:` `1rp5(B) : PTRFGLTDEYAGQLPADNIVNIAMSAFGQGISVTQTQMLRAFTAIANDGVMLEPKFISALYDPNDQSVRKSQKEIVGNPVSKEAASVTRDHMVMVGTDPTYGTMYNHSTGKATVNVPGQN` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1rp5(A) : VALKSGTAEIADEKNGGYLTGSTNNIFSVVSMHPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKESLNLQTTAKALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVV` `:` `1rp5(B) : VALKSGTAEIADEKNGGYLTGSTNNIFSVVSMHPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKESLNLQTTAKALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVV` `________________________________________________________________________________________________________________________` `_______________________________________________________________________________________` `1rp5(A) : GTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETFAKWLNIELEFEGSGSTVQKQDVRANTAIKDIKKIKLTLGD` `:` `1rp5(B) : GTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETFAKWLNIELEFEGSGSTVQKQDVRANTAIKDIKKIKLTLGD` `_______________________________________________________________________________________`

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)	5.4
Translation (A)	-0.2
Closure (%)	77.5
Bending Residues ( green )	78 - 79 88 - 89 185 - 186 196 - 198 215 - 216 222 - 223 227 - 230 257 - 258 303 - 305
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	8.7
Translation (A)	-0.1
Closure (%)	95.1
Bending Residues ( green )	92 - 95 181 - 182
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:

No Contacts

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