DynDom - Protein Domain Motions

Penicillin-Binding Protein 3

(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 3
Conformer 1 (PDB)	3oc2 (A)
Conformer 2 (PDB)	3pbn (A)
Window Length	7
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	381	0.94	63 - 81 151 - 555
2	44	0.64	82 - 150

Sequence

`_________________________76_____________________________________________________________________148_____________________` `3oc2(A) : ARSVRHIAIPAHRGLITDRNGEPLAVSTPVTTLWANPKELMTAKERWPQLAAALGQDTKLFADRIEQNAEREFIYLVRGLTPEQGEGVIALKVPGVYSIEEFRRFYPAGEVVAHAVGFTD` `:` `3pbn(A) : *********AHRGLITDRNGEPLAVSTPVTTLWANPKELMTAKERWPQLAAALGQDTKLFADRIE-------------------------kVPGVYSIEEFRRFYPAGEVVAHAVGFTD` `_________________________76_____________________________________________________________________148_____________________` `________________________________________________________________________________________________________________________` `3oc2(A) : VDDRGREGIELAFDEWLAGVPGKRQVLKDRRGRVIKDVQVTKNAKPGKTLALSIDLRLQYLAHRELRNALLENGAKAGSLVIMDVKTGEILAMTNQPTYNPNNRRNLQPAAMRNRAMIDV` `:` `3pbn(A) : VDDRGREGIELAFDEWLA-----------------------------kTLALSIDLRLQYLAHRELRNALLENGAKAGSLVIMDVKTGEILAMTNQPTYNPNNRRNLQPAAMRNRAMIDV` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `3oc2(A) : FEPGSTVKPFSMSAALASGRWKPSDIVDVYPGTLQIGRYTIRDVSRNSRQLDLTGILIKSSNVGISKIAFDIGAESIYSVMQQVGLGQDTGLGFPGERVGNLPNHRKWPKAETATLAYGY` `:` `3pbn(A) : FEPGSTVKPFSMSAALASGRWKPSDIVDVYPGTLQIGRYTIRDVSRNSRQLDLTGILIKSSNVGISKIAFDIGAESIYSVMQQVGLGQDTGLGFPGERVGNLPNHRKWPKAETATLAYGY` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `3oc2(A) : GLSVTAIQLAHAYAALANDGKSVPLSMTRVDRVPDGVQVISPEVASTVQGMLQQVVEAQGGVFRAQVPGYHAAGKSGTARK-aYRSLFAGFAPATDPRIAMVVVIDEP-----fGGLVSA` `:` `3pbn(A) : GLSVTAIQLAHAYAALANDGKSVPLSMTRVDRVPDGVQVISPEVASTVQGMLQQVVEAQGGVFRAQVPGYHAAGKSGTARKnAYRSLFAGFAPATDPRIAMVVVIDEPSKAGYFGGLVSA` `________________________________________________________________________________________________________________________` `______________________` `3oc2(A) : PVFSKVMAGALRLMNVPPDNL` `:` `3pbn(A) : PVFSKVMAGALRLMNVPPDNLP` `______________________`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
For more advanced options, right click on the model.

play backwards

pause

play forwards

Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	12.1
Translation (A)	-0.7
Closure (%)	95.6
Bending Residues ( green )	76 - 82 148 - 151
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

Download and extract PyMOL PML script file

Download