DynDom - Protein Domain Motions

Linear Gramicidin Synthase 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 Synthase Subunit A
Conformer 1 (PDB)	6mfz (A)
Conformer 2 (PDB)	5es5 (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	386	0.64	191 - 516 521 - 580
2	192	1.1	3 - 190 517 - 520
3	94	1.01	588 - 681

Sequence

`________________________________________________________________________________________________________________________` `6mfz(A) : MGRILFLTTFMSKGNKVVRYLESLHHEVVICQEKVHAQSANLQEIDWIVSYAYGYILDKEIVSRFRGRIINLHPSLLPWNKGRDPVFWSVWDETPKGVTIHLIDEHVDTGDILVQEEIAF` `:` `5es5(A) : MGRILFLTTFMSKGNKVVRYLESLHHEVVICQEKVHAQSANLQEIDWIVSYAYGYILDKEIVSRFRGRIINLHPSLLPWNKGRDPVFWSVWDETPKGVTIHLIDEHVDTGDILVQEEIAF` `________________________________________________________________________________________________________________________` `___________________________________________________________________190__________________________________________________` `6mfz(A) : ADEDTLLDCYNKANQAIEELFIREWENIVHGRIAPYRQTAGGTLHFKADRDFYKNLNMTTVRELLALKRLCAEPKRGEKPIDKTFHQLFEQQVEMTPDHVAVVDRGQSLTYKQLNERANQ` `:` `5es5(A) : ADEDTLLDCYNKANQAIEELFIREWENIVHGRIAPYRQTAGGTLHFKADRDFYKNLNMTTVRELLALKRLCAEPKRGEKPIDKTFHQLFEQQVEMTPDHVAVVDRGQSLTYKQLNERANQ` `___________________________________________________________________190__________________________________________________` `________________________________________________________________________________________________________________________` `6mfz(A) : LAHHLRGKGVKPDDQVAIMLDKSLDMIVSILAVMKAGGAYVPIDPDYPGERIAYMLADSSAAILLTNALHEEKANGACDIIDVHDPDSYSENTNNLPHVNRPDDLVYVMYTSGSTGLAKG` `:` `5es5(A) : LAHHLRGKGVKPDDQVAIMLDKSLDMIVSILAVMKAGGAYVPIDPDYPGERIAYMLADSSAAILLTNALHEEKANGACDIIDVHDPDSYSENTNNLPHVNRPDDLVYVMYTSGSTGLAKG` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6mfz(A) : VMIEHHNLVNFCEWYRPYFGVTPADKALVYSSFSFDGSALDIFTHLLAGAALHIVPSERKYDLDALNDYCNQEGITISYLPTGAAEQFMQMDNQSFRVVITGGDVLKKIERNGTYKLYNG` `:` `5es5(A) : VMIEHHNLVNFCEWYRPYFGVTPADKALVYSSFSFDGSALDIFTHLLAGAALHIVPSERKYDLDALNDYCNQEGITISYLPTGAAEQFMQMDNQSFRVVITGGDVLKKIERNGTYKLYNG` `________________________________________________________________________________________________________________________` `_________________________________516_520_________________________________________________________580____________________` `6mfz(A) : YGPTECTIMVTMFEVDKPYANIPIGKPIDRTRILILDEALALQPIGVAGELFIVGEGLGRGYLNRPELTAEKFIVHPQTGERMYRTGDRARFLPDGNIEFLGRLDNLVKIRGYRIEPGEI` `:` `5es5(A) : YGPTECTIMVTMFEVDKPYANIPIGKPIDRTRILILDEALALQPIGVAGELFIVGEGLGRGYLNRPELTAEKFIVHPQTGERMYRTGDRARFLPDGNIEFLGRLDNLVKIRGYRIEPGEI` `_________________________________516_520_________________________________________________________580____________________` `________________________________________________________________________________________________________________________` `6mfz(A) : EPFLMNHPLIELTTVLAKEQADGRKYLVGYYVAPEEIPHGELREWLGNDLPDYMIPTYFVHMKAFPLTANGKVDRRALPDVQADvAPTDELEQQLAQVWSHVLGIPQMGIDDHFLERGGD` `:` `5es5(A) : EPFLMNHPLIELTTVLAKEQADGRKYLVGYYVAPEEIPHGELREWLGNDLPDYMIPTYFVHMKAFPLTANGKVDRRALPDVQA***********************************` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6mfz(A) : SIKVMQLIHQLKNIGLSLRYDQLFTHPTIRQLKRLLTEQKQVSLEPLRELDEQAEYETSAVEKRMYIIQQQDVESIAYNVVYTINFPLTVDTEQIRVALEQLVLRHEGLRSTYHMRGDEI` `:` `5es5(A) : ********************************************************************************************************************` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6mfz(A) : VKRIVPRAELSFVRQTGEEESVQSLLAEQIKPFDLAKAPLLRAGVIETADKKVLWFDSHHILLDGLSKSILARELQALLGQQVLSPVEKTYKSFARWQNEWFASDEYEQQIAYWKTLLQG` `:` `5es5(A) : ********************************************************************************************************************` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6mfz(A) : ELPAVQLPTKKRPPQLTFDGAIQMYRVNPEITRKLKATAAKHDLTLYMLMLTIVSIWLSKMNSDSNQVILGTVTDGRQHPDTRELLGMFVNTLPLLLSIDHEESFLHNLQQVKAKLLPAL` `:` `5es5(A) : ********************************************************************************************************************` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6mfz(A) : QNQYVPFDKILEAARVKREGNRHPLFDVMFMMQGAPETELESNMHHINAGISKFDLTLEVLERENGLNIVFEYNTHLFDEGMILRMVAQFEHLLLQAVHGLDQQVKRFELVTEDEKRDLF` `:` `5es5(A) : ********************************************************************************************************************` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6mfz(A) : LRVNDTAKAYPNKLIMSMLEDWAAATPDKTALVFREQRVTYRELNERVNQLAHTLREKGVQPDDLVMLMAERSVEMMVAIFAVLKAGGAYLPIDPHSPAERIAYIFADSGAKLVLAQSPF` `:` `5es5(A) : ********************************************************************************************************************` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6mfz(A) : VEKASMAEVVLDLNSASSYAADTSNPPLVNQPGDLVYVMYTSGSTGKPKGVMIEHGALLNVLHGMQDEYPLLQDDAFLLKTTYIFDISVAEIFGWVPGRGKLVILEPEAEKNPKAIWQAV` `:` `5es5(A) : ********************************************************************************************************************` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6mfz(A) : VGAGITHINFVPSMLIPFVEYLEGRTEANRLRYILACGEAMPDELVPKVYEVLPEVKLENIYGPTEATIYASRYSLAKGSQESPVPIGKPLPNYRMYIINRHGQLQPIGVPGELCIAGAS` `:` `5es5(A) : ********************************************************************************************************************` `________________________________________________________________________________________________________________________` `________________________________________________________________________________________________________________________` `6mfz(A) : LARGYLNNPALTEEKFTPHPLEKGERIYRTGDLARYREDGNIEYLGRMDHQVKIRGYRIELDEIRSKLIQEETIQDAVVVARNDQNGQAYLCAYLLSEQEWTVGQLRELLRRELPEYMIP` `:` `5es5(A) : ********************************************************************************************************************` `________________________________________________________________________________________________________________________` `_____________________________________________________________________________________________________________` `6mfz(A) : AHFVLLKQFPLTANGKLDRKALPEaAPRTELEATLAHIWGEVLGIERIGIRDNFFELGGDSIKGLQIASRLQRINWTMVINHLFLYPTIEQIAPFVTSEQVVIEAAAEN` `:` `5es5(A) : ***********************************************************************************************************` `_____________________________________________________________________________________________________________`

Morph

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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	8.2
Translation (A)	-0.3
Closure (%)	59.2
Bending Residues ( green )	190 - 198 516 - 517 520 - 521
Bending Region Analysis

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( yellow )	3
Rotation Angle (deg)	38.5
Translation (A)	1.4
Closure (%)	97.2
Bending Residues ( green )	580 - 588
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: Hinge

PyMOL Script

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