DynDom - Protein Domain Motions

Phospholipid-Transporting Atpase Abca3

(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	Phospholipid-Transporting Atpase Abca3
Conformer 1 (PDB)	7w01 (A)
Conformer 2 (PDB)	7w02 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	184	2.18	516 - 611 667 - 668 683 - 755 831 - 841 1677 - 1678
2	345	1.47	3 - 48 253 - 490 612 - 663 669 - 677
3	73	0.8	757 - 829
4	388	1.3	842 - 943 1095 - 1330 1459 - 1558 1565 - 1565
5	61	1.23	1610 - 1676 1679 - 1682
6	325	1.4	49 - 252 951 - 1088
7	145	1.08	1357 - 1458 1559 - 1564 1566 - 1605 1686 - 1693

Sequence

`______________________________________________48________________________________________________________________________` `7w01(A) : MAVLRQLALLLWKNYTLQKRKVLVTVLELFLPLLFSGILIWLRLKIQSENVPNATIYPGQSIQELPLFFTFPPPGDTWELAYIPSHSDAAKTVTETVRRALVINMRVRGFPSEKDFEDYI` `:` `7w02(A) : MAVLRQLALLLWKNYTLQKRKVLVTVLELFLPLLFSGILIWLRLKIQSENVPNATIYPGQSIQELPLFFTFPPPGDTWELAYIPSHSDAAKTVTETVRRALVINMRVRGFPSEKDFEDYI` `______________________________________________48________________________________________________________________________` `____________________________________________________________________________________________________________________252_` `7w01(A) : RYDNCSSSVLAAVVFEHPFNHSKEPLPLAVKYHLRFSYTRRNYeGWHTTSLFPLFPNPGPREPTSPDGGEPGYIREGFLAVQHAVDRAIMEYHADAATRQLFQRLTVTIKRFPYPPFIAD` `:` `7w02(A) : RYDNCSSSVLAAVVFEHPFNHSKEPLPLAVKYHLRFSYTRRNYeGWHTTSLFPLFPNPGPREPTSPDGGEPGYIREGFLAVQHAVDRAIMEYHADAATRQLFQRLTVTIKRFPYPPFIAD` `____________________________________________________________________________________________________________________252_` `________________________________________________________________________________________________________________________` `7w01(A) : PFLVAIQYQLPLLLLLSFTYTALTIARAVVQEKERRLKEYMRMMGLSSWLHWSAWFLLFFLFLLIAASFMTLLFCVKVKPNVAVLSRSDPSLVLAFLLCFAISTISFSFMVSTFFSKANM` `:` `7w02(A) : PFLVAIQYQLPLLLLLSFTYTALTIARAVVQEKERRLKEYMRMMGLSSWLHWSAWFLLFFLFLLIAASFMTLLFCVKVKPNVAVLSRSDPSLVLAFLLCFAISTISFSFMVSTFFSKANM` `________________________________________________________________________________________________________________________` `__________________________________________________________________________________________________________________490___` `7w01(A) : AAAFGGFLYFFTYIPYFFVAPRYNWMTLSQKLCSCLLSNVAMAMGAQLIGKFEAKGMGIQWRDLLSPVNVDDDFCFGQVLGMLLLDSVLYGLVTWYMEAVFPGQFGVPQPWYFFIMPS--` `:` `7w02(A) : AAAFGGFLYFFTYIPYFFVAPRYNWMTLSQKLCSCLLSNVAMAMGAQLIGKFEAKGMGIQWRDLLSPVNVDDDFCFGQVLGMLLLDSVLYGLVTWYMEAVFPGQFGVPQPWYFFIMPSYW` `__________________________________________________________________________________________________________________490___` `_____________________________________________________________________________________________611________________________` `7w01(A) : nEYFEAEPEDLVAGIKIKHLSKVFRVGNKDRAAVRDLNLNLYEGQITVLLGHNGAGKTTTLSMLTGLFPPTSGRAYISGYEISQDMVQIRKSLGLCPQHDILFDNLTVAEHLYFYAQLKG` `:` `7w02(A) : nEYFEAEPEDLVAGIKIKHLSKVFRVGNKDRAAVRDLNLNLYEGQITVLLGHNGAGKTTTLSMLTGLFPPTSGRAYISGYEISQDMVQIRKSLGLCPQHDILFDNLTVAEHLYFYAQLKG` `_____________________________________________________________________________________________611________________________` `_________________________663___________677___________________________________________________________________________755` `7w01(A) : LSRQKCPEEVKQMLHIIGLEDKWNSRSRFLSGGMRRKLSIGIALIAGSKVLILDEPTSGMDAISRRAIWDLLQRQKSDRTIVLTTHFMDEADLLGDRIAIMAKGELQCCGSSLFLKQKYG` `:` `7w02(A) : LSRQKCPEEVKQMLHIIGLEDKWNSRSRFLSGGMRRKLSIGIALIAGSKVLILDQPTSGMDAISRRAIWDLLQRQKSDRTIVLTTHFMDEADLLGDRIAIMAKGELQCCGSSLFLKQKYG` `_________________________663___________677___________________________________________________________________________755` `_______________________________________________________________________829_________841__________________________________` `7w01(A) : AGYHMTLVKEPHCNPEDISQLVHHHVPNATLESSAGAELSFILPRESTHRFEGLFAKLEKKQKELGIASFGASITTMEEVFLRVGKLVDSSMDIQAIQLPALvKLNTGLALHCQQFWAMF` `:` `7w02(A) : AGYHMTLVKEPHCNPEDISQLVHHHVPNATLESSAGAELSFILPRESTHRFEGLFAKLEKKQKELGIASFGASITTMEEVFLRVGKLV--------------vKLNTGLALHCQQFWAMF` `_______________________________________________________________________829_________841__________________________________` `____________________________943_________________________________________________________________________________________` `7w01(A) : LKKAAYSWREWKMVAAQVLVPLTCVTLALLAINYSSELFDDPMLRLTLGEYGRTVVPFSVPGTSQLGQQLSEHLKDALQAEGQEPRE----lEEFLIFRASVEGGGFNERCLVAASFRDV` `:` `7w02(A) : LKKAAYSWREWKMVAAQVLVPLTCVTLALLAINYSSELFDDPMLRLTLGEYGRTVVPFSVPGTSQLGQQLSEHLKDALQAEGQEPREVLGDLEEFLIFRASVEGGGFNERCLVAASFRDV` `____________________________943_________________________________________________________________________________________` `______________________________________________1082______________________________________________________________________` `7w01(A) : GERTVVNALFNNQAYHSPATALAVVDNLLFKLLCGPHASIVVSNFPQPRSALQAAKDQFNEGRKGFDIALNLLFAMAFLASTFSILAVSERAVQAKHVQFVSGVHVASFWLSALLWDLIS` `:` `7w02(A) : GERTVVNALFNNQAYHSPATALAVVDNLLFKLLCGPHASIVVSNFPQPRSALQAAKDQFNEGRKGFDIALNLLFAMAFLASTFSILAVSERAVQAKHVQFVSGVHVASFWLSALLWDLIS` `______________________________________________1082______________________________________________________________________` `________________________________________________________________________________________________________________________` `7w01(A) : FLIPSLLLLVVFKAFDVRAFTRDGHMADTLLLLLLYGWAIIPLMYLMNFFFLGAATAYTRLTIFNILSGIATFLMVTIMRIPAVKLEELSKTLDHVFLVLPNHCLGMAVSSFYENYETRR` `:` `7w02(A) : FLIPSLLLLVVFKAFDVRAFTRDGHMADTLLLLLLYGWAIIPLMYLMNFFFLGAATAYTRLTIFNILSGIATFLMVTIMRIPAVKLEELSKTLDHVFLVLPNHCLGMAVSSFYENYETRR` `________________________________________________________________________________________________________________________` `___________________________________________________1327_________________________________________________________________` `7w01(A) : YCTSSEVAAHYCKKYNIQYQENFYAWSAPGVGRFVASMAASGCAYLILLFLIETNLLQRLlPEDQDVADERTRILAPSPDSLLHTPLIIKELSKVYEQRVPLLAVDRLSLAVQKGECFGL` `:` `7w02(A) : YCTSSEVAAHYCKKYNIQYQENFYAWSAPGVGRFVASMAASGCAYLILLFLIETNLLQRLlPEDQDVADERTRILA-----lLHTPLIIKELSKVYEQRVPLLAVDRLSLAVQKGECFGL` `___________________________________________________1327_________________________________________________________________` `________________________________________1458____________________________________________________________________________` `7w01(A) : LGFNGAGKTTTFKMLTGEESLTSGDAFVGGHRISSDVGKVRQRIGYCPQFDALLDHMTGREMLVMYARLRGIPERHIGACVENTLRGLLLEPHANKLVRTYSGGNKRKLSTGIALIGEPA` `:` `7w02(A) : LGFNGAGKTTTFKMLTGEESLTSGDAFVGGHRISSD------rIGYCPQFDALLDHMTGREMLVMYARLRGIPERHIGACVENTLRGLLLEPHANKLVRTYSGGNKRKLSTGIALIGEPA` `________________________________________1458____________________________________________________________________________` `____________________1558__1564__________________________________1602____________________________________________________` `7w01(A) : VIFLDEPSTGMDPVARRLLWDTVARARESGKAIIITSHSMEECEALCTRLAIMVQGQFKCLGSPQHLKSKFGSGYSLRAKVQSEGQQEALEEFKAFVDLTFPGSVLEDEHQGMVHYHLPG` `:` `7w02(A) : VIFLDQPSTGMDPVARRLLWDTVARARESGKAIIITSHSMEECEALCTRLAIMVQGQFKCLGSPQHLKSKFGSGYSLRAKV-----qEALEEFKAFVDLTFPGSVLEDEHQGMVHYHLP-` `____________________1558__1564__________________________________1602____________________________________________________` `__________________1676__1682________________` `7w01(A) :` `RDLSWAKVFGILEKAKEKYGVDDYSVSQISLEQVFLSFAHLQPP` `:` `7w02(A) :` `----wAKVFGILEKAKEKYGVDDYSVSQISLEQVFLSFAHL***` `__________________1676__1682________________`

Morph

Jmol._Canvas2D (Jmol) "jmolApplet"[x]

Morph animation in progress.
Status: Initialising

This morph was created using the MorphIt_Pro protein morphing technique.
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Domain Pairs

Fixed Domain	Moving Domain	Rotation Angle	Translation (A)	Closure	Bending Residues
1	2	30.4	0.0	10.0	490 - 517 611 - 612 663 - 669 677 - 683	Bending Region Analysis
1	3	36.7	-0.2	86.7	755 - 757 829 - 831	Bending Region Analysis
1	4	30.7	2.5	99.1	841 - 842	Bending Region Analysis
1	5	22.5	4.6	10.4	1676 - 1679	Bending Region Analysis
6	2	33.6	-0.2	16.3	48 - 49 252 - 262	Bending Region Analysis
6	4	45.4	-0.9	22.4	943 - 952 1082 - 1095	Bending Region Analysis
7	4	23.4	0.2	11.3	1327 - 1358 1458 - 1459 1558 - 1559 1564 - 1566	Bending Region Analysis
7	5	47.6	2.3	57.5	1602 - 1610 1682 - 1688	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

Conformer 1 Contact:
Residue 1 ———› Residue 4

Conformer 2 Contact:
Residue 4 ———› Residue 1

Movement classification: Hinge

Conformer 1 Contact:
Residue 1 ———› Residue 5

Conformer 2 Contact:
Residue 5 ———› Residue 1

Movement classification: Hinge

Conformer 1 Contact:
Residue 6 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 6

Movement classification:

No Contacts

Conformer 1 Contact:
Residue 6 ———› Residue 4

Conformer 2 Contact:
Residue 4 ———› Residue 6

Movement classification:

No Contacts

Conformer 1 Contact:
Residue 7 ———› Residue 4

Conformer 2 Contact:
Residue 4 ———› Residue 7

Movement classification: Hinge

Conformer 1 Contact:
Residue 7 ———› Residue 5

Conformer 2 Contact:
Residue 5 ———› Residue 7

Movement classification:

No Contacts

PyMOL Script

Download and extract PyMOL PML script file

Phospholipid-Transporting Atpase Abca3

DynDom run details

Domains

Sequence

Morph

Domain Pairs

Dynamic Contact Graph

Full-size image

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

Conformer 1 Contact:Residue 1 ———› Residue 4

Conformer 2 Contact:Residue 4 ———› Residue 1

Movement classification: Hinge

Conformer 1 Contact:Residue 1 ———› Residue 5

Conformer 2 Contact:Residue 5 ———› Residue 1

Movement classification: Hinge

Conformer 1 Contact:Residue 6 ———› Residue 2

Conformer 2 Contact:Residue 2 ———› Residue 6

Movement classification:

No Contacts

Conformer 1 Contact:Residue 6 ———› Residue 4

Conformer 2 Contact:Residue 4 ———› Residue 6

Movement classification:

No Contacts

Conformer 1 Contact:Residue 7 ———› Residue 4

Conformer 2 Contact:Residue 4 ———› Residue 7

Movement classification: Hinge

Conformer 1 Contact:Residue 7 ———› Residue 5

Conformer 2 Contact:Residue 5 ———› Residue 7

Movement classification:

No Contacts

PyMOL Script

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

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

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

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

Conformer 1 Contact:
Residue 1 ———› Residue 4

Conformer 2 Contact:
Residue 4 ———› Residue 1

Conformer 1 Contact:
Residue 1 ———› Residue 5

Conformer 2 Contact:
Residue 5 ———› Residue 1

Conformer 1 Contact:
Residue 6 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 6

Conformer 1 Contact:
Residue 6 ———› Residue 4

Conformer 2 Contact:
Residue 4 ———› Residue 6

Conformer 1 Contact:
Residue 7 ———› Residue 4

Conformer 2 Contact:
Residue 4 ———› Residue 7

Conformer 1 Contact:
Residue 7 ———› Residue 5

Conformer 2 Contact:
Residue 5 ———› Residue 7