DynDom - Protein Domain Motions

Penicillin-Binding Protein 2A

(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 2A
Conformer 1 (PDB)	1mwr (B)
Conformer 2 (PDB)	1vqq (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	422	0.84	148 - 170 176 - 181 186 - 192 213 - 214 222 - 228 233 - 262 273 - 291 319 - 666
2	146	0.89	29 - 147 263 - 272 292 - 318
3	38	0.41	171 - 175 182 - 185 193 - 212 215 - 221 229 - 232

Sequence

`________________________________________________________________________________________________________________147_____` `1mwr(B) : DKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVE-tERPIKIYNSLGVKDINIQDRKIKKrVDAQYKIKTNYGNIDRNVQFNFVKEDG-wKLDWDHSVIIPG-qKDQSIHIENLKSERG` `:` `1vqq(B) : DKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKrVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIENLKSERG` `________________________________________________________________________________________________________________147_____` `_______________170__175___181_185____192_________________212_____221_____228_232________________________259__________272` `1mwr(B) : KILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQ-dQNWVQDDTFVPLKTVKK-dEYLSDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGY` `:` `1vqq(B) : KILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQKEYKGY` `_______________170__175___181_185____192_________________212_____221_____228_232________________________259__________272` `________________291_______________________318___________________________________________________________________________` `1mwr(B) : KDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDsNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNN-kNDYGSGTAIHPQTGELLALVSTPSYDVYPF-yG-sNEEYNKLTEDKKEPLLN` `:` `1vqq(B) : KDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDsNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTEDKKEPLLN` `________________291_______________________318___________________________________________________________________________` `________________________________________________________________________________________________________________________` `1mwr(B) : KFQITTSPGSTQKILTA-iGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKG-kKLGVGEDIPSDYPFYNAQISNKNLDNEIL` `:` `1vqq(B) : KFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQI----lDNEIL` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1mwr(B) : LADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDG-qQVVNKTHKEDIYRSYANLIGKSGTAELKgRQIGWFISYDKDNPN---aINVKDVQDK` `:` `1vqq(B) : LADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKgRQIGWFISYDKDNPNMMMAINVKDVQDK` `________________________________________________________________________________________________________________________` `_____________________________` `1mwr(B) : G-aSYNAKISGKVYDELYENGNKKYDIDE` `:` `1vqq(B) : GMASYNAKISGKVYDELYENGNKKYDIDE` `_____________________________`

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)	9.6
Translation (A)	0.1
Closure (%)	94.4
Bending Residues ( green )	147 - 148 259 - 264 272 - 275 291 - 292 318 - 319
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	6.4
Translation (A)	0.4
Closure (%)	65.9
Bending Residues ( green )	170 - 171 175 - 176 181 - 182 185 - 186 192 - 193 212 - 215 221 - 222 228 - 229 232 - 233
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Mixed

Conformer 1 Contact:
Residue 1 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 1

Movement classification: Shear

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