DynDom - Protein Domain Motions

DNA Ligase

(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	DNA Ligase
Conformer 1 (PDB)	1dgs (A)
Conformer 2 (PDB)	1dgs (B)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	343	0.66	4 - 269 277 - 282 284 - 312 321 - 332 336 - 336 339 - 343 353 - 356 363 - 363 366 - 367 375 - 384 408 - 408 414 - 419
2	232	0.8	270 - 276 283 - 283 313 - 320 333 - 335 337 - 338 344 - 352 357 - 362 364 - 365 368 - 374 385 - 407 409 - 413 420 - 578

Sequence

`________________________________________________________________________________________________________________________` `1dgs(A) : MTREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGARPLEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERLEREAEAPSLYTVEHKVDGL` `:` `1dgs(B) : MTREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGARPLEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERLEREAEAPSLYTVEHKVDGL` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `1dgs(A) : SVLYYEEGVWSTGSGDGEVGEEVTQNLLTIPTIPRRLKGVPDRLEVRGEVYMPIEAFLRLNEELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLGLEESGLKSQYEL` `:` `1dgs(B) : SVLYYEEGVWSTGSGDGEVGEEVTQNLLTIPTIPRRLKGVPDRLEVRGEVYMPIEAFLRLNEELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLGLEESGLKSQYEL` `________________________________________________________________________________________________________________________` `__________________________269____276___282___________________________312_____320_________332________343______352_356___3` `1dgs(A) : LLWLKEKGFPVEHCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKLDDLTLWGELGYTARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHNES` `:` `1dgs(B) : LLWLKEKGFPVEHCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKLDDLTLWGELGYTARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHNES` `_________________________2269___2276__2282__________________________2312____2320________2332_______2343_____2352______23` `62_________374_______384____________________407___413___419_____________________________________________________________` `1dgs(A) : YIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGKERPIRWPEACPECGHRLVKEGKVHRCPNPLCPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRKEDLLGL` `:` `1dgs(B) : YIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGKERPIRWPEACPECGHRLVKEGKVHRCPNPLCPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRKEDLLGL` `62________2374______2384___________________2407__2413__2419_____________________________________________________________` `_____________________________________________________________________________________________________` `1dgs(A) : ERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEASLEELIEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVSMESK` `:` `1dgs(B) : ERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEASLEELIEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVSMESK` `_____________________________________________________________________________________________________`

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)	3.1
Translation (A)	-0.2
Closure (%)	46.3
Bending Residues ( green )	269 - 270 276 - 277 282 - 284 312 - 318 320 - 321 332 - 333 335 - 339 343 - 344 352 - 353 356 - 357 362 - 368 374 - 375 384 - 385 407 - 409 413 - 414 419 - 420
Bending Region Analysis

Dynamic Contact Graph

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

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

Movement classification: Shear

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