DynDom - Protein Domain Motions

Outer Membrane Protein Assembly Factor Bama

(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	Outer Membrane Protein Assembly Factor Bama
Conformer 1 (PDB)	5d0o (A)
Conformer 2 (PDB)	5ljo (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	170	2.21	173 - 246 252 - 347
2	150	1.79	26 - 172 249 - 251
3	103	1.05	348 - 424 444 - 458 472 - 482
4	350	4.48	425 - 443 459 - 471 487 - 804

Sequence

`________________________________________________________________________________________________________________________` `5d0o(A) : FVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDFYYS` `:` `5ljo(A) : FVVKDIHFEGLQRVAVGAALLSMPVRTGDTVNDEDISNTIRALFATGNFEDVRVLRDGDTLLVQVKERPTIASITFSGNKSVKDDMLKQNLEASGVRVGESLDRTTIADIEKGLEDFYYS` `________________________________________________________________________________________________________________________` `__________________________172_______________________________________________________________________246_________________` `5d0o(A) : VGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNITEG` `:` `5ljo(A) : VGKYSASVKAVVTPLPRNRVDLKLVFQEGVSAEIQQINIVGNHAFTTDELISHFQLRDEVPWWNVVGDRKYQKQKLAGDLETLRSYYLDRGYARFNIDSTQVSLTPDKKGIYVTVNITEG` `__________________________172_______________________________________________________________________246_________________` `_________________________________________________________________________________347____________________________________` `5d0o(A) : DQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVNVDAGNRFYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSDLVD` `:` `5ljo(A) : DQYKLSGVEVSGNLAGHSAEIEQLTKIEPGELYNGTKVTKMEDDIKKLLGRYGYAYPRVQSMPEINDADKTVKLRVNVDAGNRFYVRKIRFEGNDTSKDAVLRREMRQMEGAWLGSDLVD` `_________________________________________________________________________________347____________________________________` `______________________________________424________________443___________457___________471_______481______________________` `5d0o(A) : QGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKERNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDADLSD` `:` `5ljo(A) : QGKERLNRLGFFETVDTDTQRVPGSPDQVDVVYKVKERNTGSFNFGIGYGTESGVSFQAGVQQDNWLGTGYAVGINGTKNDYQTYAELSVTNPYFTVDGVSLGGRLFYNDFQADDADLSD` `______________________________________424________________443___________457___________471_______481______________________` `________________________________________________________________________________________________________________________` `5d0o(A) : YTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVPIDD` `:` `5ljo(A) : YTNKSYGTDVTLGFPINEYNSLRAGLGYVHNSLSNMQPQVAMWRYLYSMGEHPSTSDQDNSFKTDDFTFNYGWTYNKLDRGYFPTDGSRVNLTGKVTIPGSDNEYYKVTLDTATYVPIDD` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `5d0o(A) : DHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWDMGT` `:` `5ljo(A) : DHKWVVLGRTRWGYGDGLGGKEMPFYENFYAGGSSTVRGFQSNTIGPKAVYFPHQASNYDPDYDYECATQDGAKDLCKSDDAVGGNAMAVASLEFITPTPFISDKYANSVRTSFFWDMGT` `________________________________________________________________________________________________________________________` `__________________________________________________________________` `5d0o(A) : VWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAEQFQFNIGKT` `:` `5ljo(A) : VWDTNWDSSQYSGYPDYSDPSNIRMSAGIALQWMSPLGPLVFSYAQPFKKYDGDKAEQFQFNI***` `__________________________________________________________________`

Morph

Morph animation in progress.
Status: Initialising

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

Fixed Domain	Moving Domain	Rotation Angle	Translation (A)	Closure	Bending Residues
1	2	38.6	-3.1	16.5	172 - 173 246 - 252	Bending Region Analysis
1	3	25.7	-5.8	87.2	347 - 348	Bending Region Analysis
4	3	43.5	-0.2	47.1	424 - 425 443 - 444 457 - 459 471 - 472 481 - 487	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: Hinge

Conformer 1 Contact:
Residue 4 ———› Residue 3

Conformer 2 Contact:
Residue 3 ———› Residue 4

Movement classification: Hinge

PyMOL Script

Download and extract PyMOL PML script file

Download