DynDom - Protein Domain Motions

Linear Gramicidin Synthetase Subunit A

(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	Linear Gramicidin Synthetase Subunit A
Conformer 1 (PDB)	5es8 (A)
Conformer 2 (PDB)	5es9 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	91	0.43	589 - 679
2	579	0.76	3 - 585
3	76	1.32	693 - 768

Sequence

`________________________________________________________________________________________________________________________` `5es8(A) : MGRILFLTTFMSKGNKVVRYLESLHHEVVICQEKVHAQSANLQEIDWIVSYAYGYILDKEIVSRFRGRIINLHPSLLPWNKGRDPVFWSVWDETPKGVTIHLIDEHVDTGDILVQEEIAF` `:` `5es9(A) : MGRILFLTTFMSKGNKVVRYLESLHHEVVICQEKVHAQSANLQEIDWIVSYAYGYILDKEIVSRFRGRIINLHPSLLPWNKGRDPVFWSVWDETPKGVTIHLIDEHVDTGDILVQEEIAF` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `5es8(A) : ADEDTLLDCYNKANQAIEELFIREWENIVHGRIAPYRQTAGGTLHFKADRDFYKNLNMTTVRELLALKRLCAEPKRGEKPIDKTFHQLFEQQVEMTPDHVAVVDRGQSLTYKQLNERANQ` `:` `5es9(A) : ADEDTLLDCYNKANQAIEELFIREWENIVHGRIAPYRQTAGGTLHFKADRDFYKNLNMTTVRELLALKRLCAEPKRGEKPIDKTFHQLFEQQVEMTPDHVAVVDRGQSLTYKQLNERANQ` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `5es8(A) : LAHHLRGKGVKPDDQVAIMLDKSLDMIVSILAVMKAGGAYVPIDPDYPGERIAYMLADSSAAILLTNALHEEKANGACDIIDVHDPDSYSENTNNLPHVNRPDDLVYVMYTSGSTGLAKG` `:` `5es9(A) : LAHHLRGKGVKPDDQVAIMLDKSLDMIVSILAVMKAGGAYVPIDPDYPGERIAYMLADSSAAILLTNALHEEKANGACDIIDVHDPDSYSENTNNLPHVNRPDDLVYVMYTS----lAKG` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `5es8(A) : VMIEHHNLVNFCEWYRPYFGVTPADKALVYSSFSFDGSALDIFTHLLAGAALHIVPSERKYDLDALNDYCNQEGITISYLPTGAAEQFMQMDNQSFRVVITGGDVLKKIERNGTYKLYNG` `:` `5es9(A) : VMIEHHNLVNFCEWYRPYFGVTPADKALVYSSFSFDGSALDIFTHLLAGAALHIVPSERKYDLDALNDYCNQEGITISYLPTGAAEQFMQMDNQSFRVVITGGDVLKKIERNGTYKLYNG` `________________________________________________________________________________________________________________________` `___________________________________________________________________________________________________582__________________` `5es8(A) : YGPTECTIMVTMFEVDKPYANIPIGKPIDRTRILILDEALALQPIGVAGELFIVGEGLGRGYLNRPELTAEKFIVHPQTGERMYRTGDRARFLPDGNIEFLGRLDNLVKIRGYRIEPGEI` `:` `5es9(A) : YGPTECTIMVTMFEVDKPYANIPIGKPIDRTRILILDEALALQPIGVAGELFIVGEGLGRGYLNRPELTAEKFIVHPQTGERMYRTGDRARFLPDGNIEFLGRLDNLVKIRGYRIEPGEI` `___________________________________________________________________________________________________582__________________` `______________________________________________________________________673_______________________________________________` `5es8(A) : EPFLMNHPLIELTTVLAKEQADGRKYLVGYYVAPEEIPHGELREWLGNDLPDYMIPTYFVHMKAFPLTANGKVDRRALPDV----vAPTDELEQQLAQVWSHVLGIPQMGIDDHFLERGG` `:` `5es9(A) : EPFLMNHPLIELTTVLAKEQADGRKYLVGYYVAPEEIPHGELREWLGNDLPDYMIPTYFVHMKAFPLTANGKVDRRALPDVQADAvAPTDELEQQLAQVWSHVLGIPQMGIDDHFLERGG` `______________________________________________________________________673_______________________________________________` `___________________________________________` `5es8(A) : DSIKVMQLIHQLKNIGLSLRYDQLFTHPTIRQLKRLLTEQAAA` `:` `5es9(A) : DSIKVMQLIHQLKNIGLSLRYDQLFTHPTIRQLKRLLTEQAAA` `___________________________________________`

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)	156.5
Translation (A)	3.4
Closure (%)	33.1
Bending Residues ( green )	582 - 589
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	83.2
Translation (A)	24.7
Closure (%)	47.8
Bending Residues ( green )	673 - 694
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

PyMOL Script

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