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

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Jmol applet jmolApplet1__003943604757933__ 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__003943604757933__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__003943604757933__)

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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

defaults = "Jmol"

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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__003943604757933__ ready

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Viewer cachePut cache://localLOAD_/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): 395 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: 39 ms

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

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Script completed

Jmol script terminated

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

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): 18 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: 20 ms

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

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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

script 1 started

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Jmol JavaScript applet jmolApplet2__003943604757933__ initializing

Jmol getValue debug null

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AppletRegistry.checkIn(jmolApplet2__003943604757933__)

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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

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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

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Jmol getValue SCRIPTCallback null

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Jmol getValue STRUCTUREMODIFIEDCallback null

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language=en_US

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Jmol applet jmolApplet2__003943604757933__ 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

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

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

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

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

...loading similar chains, please wait...
similar chains in the KnotProt database (?% sequence similarity)

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similar chains in the pdb database (?% sequence similarity)

#similar chains in the KnotProt database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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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