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 (A)
Conformer 2 (PDB)	3zg0 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	361	0.74	143 - 297 302 - 308 317 - 396 408 - 412 489 - 498 529 - 530 534 - 537 546 - 554 557 - 572 576 - 666
2	117	0.45	29 - 142 298 - 301 309 - 316
3	127	0.59	397 - 407 413 - 488 499 - 528 531 - 533 538 - 545 555 - 556 573 - 574

Sequence

`_________________________________________________________________________________________________________________142____` `1mwr(A) : DKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVE-tERPIKIYNSLGVKDINIQDRKIKK------rVDAQYKIKTNYGNIDRNVQFNFVKEDG-wKLDWDHSVIIPG-qKDQSIHIEN` `:` `3zg0(A) : DKEINNTIDAIEDKNFKQVYKDSSYISKSDNGEVEMTERPIKIYNSLGVKDINIQDRKIKKVSKNKKRVDAQYKIKTNYGNIDRNVQFNFVKEDGMWKLDWDHSVIIPGMQKDQSIHIEN` `_________________________________________________________________________________________________________________142____` `________________________________________________________________________________________________________________________` `1mwr(A) : LKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQ-dQNWVQDDTFVPLKTVKK-dEYLSDFAKKFHLTTNETESRNYPLEKATSHLLGYVGPINSEELKQ` `:` `3zg0(A) : LKSERGKILDRNNVELANTGTAYEIGIVPKNVSKKDYKAIAKELSISEDYIKQQMDQNWVQDDTFVPLKTVKKMDEYLSDFAKKFHLTTNETESRNYPLGKATSHLLGYVGPINSEELKQ` `________________________________________________________________________________________________________________________` `____________________________297_301____308_____316______________________________________________________________________` `1mwr(A) : KEYKGYKDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDD-sNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNN-kNDYGSGTAIHPQTGELLALVSTPSYDVYPF-yG-sNEEYNKLTED` `:` `3zg0(A) : KEYKGYkDDAVIGKKGLEKLYDKKLQHEDGYRVTIVDDNSNTIAHTLIEKKKKDGKDIQLTIDAKVQKSIYNNMKNDYGSGTAIHPQTGELLALVSTPSYDVYPFMYGMSNEEYNKLTED` `____________________________297_301____308_____316______________________________________________________________________` `_______396________407_412__________________________________________________________________________488_______498________` `1mwr(A) : KKEPLLNKFQITTSPGSTQKILTA-iGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKG-kKLGVGEDIPSDYPFYNAQI---` `:` `3zg0(A) : KKEPLLNKFQITTSPGSTQKILTAMIGLNNKTLDDKTSYKIDGKGWQKDKSWGGYNVTRYEVVNGNIDLKQAIESSDNIFFARVALELGSKKFEKGMKKLGVGEDIPSDYPFYNAQISNK` `_______396________407_412__________________________________________________________________________488_______498________` `___________________528__533_537_____545______554_______________572______________________________________________________` `1mwr(A) :` `-lDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDG-qQVVNKTHKEDIYRSYANLIGKSGTAELK-------rQIGWFISYDKDNPN` `:` `3zg0(A) :` `NLDNEILLADSGYGQGEILINPVQILSIYSALENNGNINAPHLLKDTKNKVWKKNIISKENINLLTDGMQQVVNKTHKEDIYRSYANLIGKSGTAELKMKQGETGRQIGWFISYDKDNPN` `___________________528__533_537_____545______554_______________572______________________________________________________` `__________________________________________` `1mwr(A) :` `---aINVKDVQDKG-aSYNAKISGKVYDELYENGNKKYDIDE` `:` `3zg0(A) :` `MMMAINVKDVQDKGMASYNAKISGKVYDELYENGNKKYDIDE` `__________________________________________`

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)	7.4
Translation (A)	0.4
Closure (%)	83.8
Bending Residues ( green )	142 - 143 297 - 298 301 - 302 308 - 309 316 - 317
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	4.6
Translation (A)	-0.3
Closure (%)	95.1
Bending Residues ( green )	396 - 397 407 - 408 412 - 413 488 - 489 498 - 499 528 - 531 533 - 534 537 - 538 545 - 546 554 - 557 572 - 576
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

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

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

Movement classification: Shear

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