1QMG | KnotProt

Genus: 210

Slipknot S 4₁ +3₁

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Jmol Version: 14.29.13 2018-04-17 17:17

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Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

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Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

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Jmol getValue MINIMIZATIONCallback null

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Jmol applet jmolApplet1__510478481051181__ ready

Help Knotting data interpretation Full screen

					Knot core range	Knot core length	Knot tails range	Slipknot tails range	Slipknot loops range	N-end length	C-end length	Type
view details				+3₁	271-388	118		1-246, 449-514	247-270, 389-448	246	66	slipknot
view details				4₁	237-444	208	1-236, 445-514			236	69	slipknot

Chain Sequence

SATTFDFDSSVFKKEKVTLSGHDEYIVRGGRNLFPLLPDAFKGIKQIGVIGWGSQAPAQAQNLKDSLTEAKSDVVVKIGLRKGSNSFAEARAAGFSEENGTLGDMWETISGSDLVLLLISDSAQADNYEKVFSHMKPNSILGLSHGFLLGHLQSLGQDFPKNISVIAVCPKGMGPSVRRLYVQGKEVNGAGINSSFAVHQDVDGRATDVALGWSIALGSPFTFATTLEQEYKSDIFGERGILLGAVHGIVECLFRRYTESGMSEDLAYKNTVECITGVISKTISTKGMLALYNSLSEEGKKDFQAAYSASYYPSMDILYECYEDVASGSEIRSVVLAGRRFYEKEGLPAFPMGKIDQTRMWKVGEKVRSVRPAGDLGPLYPFTAGVYVALMMAQIEILRKKGHSYSEIINESVIEAVDSLNPFMHARGVSFMVDNCSTTARLGSRKWAPRFDYILSQQALVAVDNGAPINQDLISNFLSDPVHEAIGVCAQLRPSVDISVTADADFVRPELRQA

Note, that the numbers in the matrix denote the consecutive residues in the loop, not the index of amino acids in the chain!

Knot K 1x 4₁ +3₁

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loadScript /static/js/j2s/core/corescript.z.js

JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__510478481051181__ initializing

Jmol getValue debug null

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Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__510478481051181__)

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setting document base to "https://knotprot.cent.uw.edu.pl/view/1qmg/A/"

Jmol Version: 14.29.13 2018-04-17 17:17

java.vendor: Java2Script (HTML5)

java.version: 2018-01-28 23:38:52 (JSmol/j2s)

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Jmol getValue emulate null

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Jmol getValue bgcolor white

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Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue AUDIOCallback null

Jmol getValue CLICKCallback null

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Jmol applet jmolApplet0__510478481051181__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/static/knot_data/1qmg/A/1qmg_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/1qmg/A/1qmg_A.pdb.gz

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FileManager.getAtomSetCollectionFromFile(/static/knot_data/1qmg/A/1qmg_A.pdb.gz)

The Resolver thinks Pdb

loadScript /static/js/j2s/core/corebio.z.js

Time for openFile(/static/knot_data/1qmg/A/1qmg_A.pdb.gz): 653 ms

reading 514 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

514 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 32 ms

Adding embedded #jmolscript: select ({0:513});backbone only;select *;

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Script completed

Jmol script terminated

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loadScript /static/js/j2s/J/renderbio/BioMeshRenderer.js

loadScript /static/js/j2s/J/render/MeshRenderer.js

loadScript /static/js/j2s/J/shape/Mesh.js

FileManager.getAtomSetCollectionFromFile(/static/knot_data/1qmg/A/1qmg_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/1qmg/A/1qmg_A.pdb.gz): 29 ms

reading 514 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

514 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 23 ms

Adding embedded #jmolscript: select ({0:513});backbone only;select *;

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cartoonsFancy = true

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Script completed

Jmol script terminated

Help Knotting data interpretation Full screen

				Knot core range	Knot core length	Knot tails range	Slipknot tails range	Slipknot loops range	N-end length	C-end length	Type
view details			4₁	236-443	208	1-235, 444-512			235	69	knot
view details			+ 3₁	270-385	116		1-244, 444-512	245-269, 386-443	244	69	slipknot

			Fingerprint	Knot forming loop	Loop type
knots details			K 4₁ +3₁	Chain closureSer82 <-> Ala595 ... Glu319 <-> Bridging ionMn601 <-> Asp315 ... Ser82	probabilistic	color sequence

Chain Sequence

Whole chain analysis

Help Knotoid data interpretation Full screen

Subchain analysis

Knotoid cutoff: 0.5

Knotoid matrix content: 1

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Jmol JavaScript applet jmolApplet2__510478481051181__ initializing

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AppletRegistry.checkIn(jmolApplet2__510478481051181__)

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setting document base to "https://knotprot.cent.uw.edu.pl/view/1qmg/A/"

Jmol Version: 14.29.13 2018-04-17 17:17

java.vendor: Java2Script (HTML5)

java.version: 2018-01-28 23:38:52 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet2 (signed)

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor white

backgroundColor = "white"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue AUDIOCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue SERVICECallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

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Jmol getValue STRUCTUREMODIFIEDCallback null

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Jmol applet jmolApplet2__510478481051181__ ready

Help Knotoid subchains data interpretation Full screen

		Knot core range	Knot core length	Knot tails range	Slipknot tails range	Slipknot loops range	N-end length	C-end length	Type
view details	4.1	235-456	222	1-234, 457-514			234	58	knot
view details	3.2	235-438	204	1-234	457-514	439-456	234	58	slipknot
view details	3.2	244-460	217		1-234, 490-514	235-243, 461-489	234	25	slipknot
view details	2.3	247-435	189		1-234, 451-514	235-246, 436-450	234	64	slipknot
view details	2.3	247-450	204		1-234, 452-514	235-246, 451-451	234	63	slipknot
view details	2.1	276-413	138		1-243, 436-514	244-275, 414-435	243	79	slipknot
view details	3.1	276-435	160		1-246, 439-514	247-275, 436-438	246	76	slipknot
view details	2.1	272-438	167		1-246, 440-514	247-271, 439-439	246	75	slipknot
view details	2.1	271-439	169		1-247, 441-514	248-270, 440-440	247	74	slipknot
view details	2.1	271-440	170		1-248, 449-514	249-270, 441-448	248	66	slipknot
view details	3.1	270-388	119		1-250, 414-514	251-269, 389-413	250	101	slipknot

sequence length	514
structure length	514
publication title	Structure of Spinach Acetohydroxyacid Isomeroreductase Complexed with its Product of Reaction Dihydroxy-Methylvalerate, Manganese and Adp-Ribose pubmed doi rcsb
molecule tags	Oxidoreductase
molecule keywords	ACETOHYDROXY-ACID ISOMEROREDUCTASE
source organism	Spinacia oleracea
total genus	Genus: 210
ec nomenclature	ec 1.1.1.86: Ketol-acid reductoisomerase.
pdb deposition date	1999-09-28
KnotProt deposition date	2018-10-20

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01450	IlvC	Acetohydroxy acid isomeroreductase, catalytic domain

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2	1qmgA02
3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	1qmgA01
1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2	1qmgA02
3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	1qmgA01

3FR7A 1QMGA 3ULKA 1R4MB 1YVEI 1YRLA 3FR8A 1R4NB
chains in the KnotProt database with same CATH superfamily

1II9A 2XTJA 3FR7A 1KI6A 1KI7A 3VTKA 1KI8A 2VTKA 3KZOA 1R4MB 1GKUB 3KZCA 1KI4A 1JS1X 1R4NB 1P73A 1E2NA 3KZMA 3L02A 3M4JA 1P72A 1KI6B 3M5CA 3L06A 3KZKA 1VTKA 1YRLA 3FR8A 3RDPA 1E2LA 1E2IA 1OSNA 3KZNA 3F0TA 3M5DA 4IVPA 1E2JA 1E2HA 1KI2A 1KIMA 1E2KA 1OF1A 3L05A 4IVQA 1DBIA 4JBXA 4JBYA 1QHIA 1P6XA 3L04A 2G7MC 1KI3A 3FSGA 1YH1A 2FG6C 2KI5A 1P75A 3M4NA 1QMGA 3ULKA 1YVEI 1E2MA 4IVRA 1F48A 1LNSA 1P7CA 1E2PA
chains in the KnotProt database with same CATH topology

3FR7A 1QMGA 3ULKA 1R4MB 1YVEI 1YRLA 3FR8A 1R4NB
chains in the KnotProt database with same CATH homology

#chains in the KnotProt database with same CATH superfamily
 3FR7 A;  1QMG A;  3ULK A;  1R4M B;  1YVE I;  1YRL A;  3FR8 A;  1R4N B; 
#chains in the KnotProt database with same CATH topology
 1II9 A;  2XTJ A;  3FR7 A;  1KI6 A;  1KI7 A;  3VTK A;  1KI8 A;  2VTK A;  3KZO A;  1R4M B;  1GKU B;  3KZC A;  1KI4 A;  1JS1 X;  1R4N B;  1P73 A;  1E2N A;  3KZM A;  3L02 A;  3M4J A;  1P72 A;  1KI6 B;  3M5C A;  3L06 A;  3KZK A;  1VTK A;  1YRL A;  3FR8 A;  3RDP A;  1E2L A;  1E2I A;  1OSN A;  3KZN A;  3F0T A;  3M5D A;  4IVP A;  1E2J A;  1E2H A;  1KI2 A;  1KIM A;  1E2K A;  1OF1 A;  3L05 A;  4IVQ A;  1DBI A;  4JBX A;  4JBY A;  1QHI A;  1P6X A;  3L04 A;  2G7M C;  1KI3 A;  3FSG A;  1YH1 A;  2FG6 C;  2KI5 A;  1P75 A;  3M4N A;  1QMG A;  3ULK A;  1YVE I;  1E2M A;  4IVR A;  1F48 A;  1LNS A;  1P7C A;  1E2P A; 
#chains in the KnotProt database with same CATH homology
 3FR7 A;  1QMG A;  3ULK A;  1R4M B;  1YVE I;  1YRL A;  3FR8 A;  1R4N B;

1YVEI 3FR7A 3FR8A
similar chains in the KnotProt database (40% sequence similarity)

9BAGA
similar chains in the pdb database (40% sequence similarity)

#similar chains in the KnotProt database (40% sequence similarity)
1YVE I; 3FR7 A; 3FR8 A; 
#similar chains, but unknotted

#similar chains in the pdb database (40% sequence similarity)
9BAG A;

1QMGA

Slipknot S 41 +31

Chain Sequence

Knot K 1x 41 +31

Chain Sequence

pfam database annotations

Slipknot S 4₁ +3₁

Knot K 1x 4₁ +3₁