3IFW | KnotProt

Genus: 69

Knot K -5₂ -3₁ -3₁

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

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callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

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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				-5₂	5-220	216	1-4, 221-223			4	3	knot
view details				-3₁	5-164	160	1-4	218-223	165-217	4	6	slipknot

Chain Sequence

MQLKPMEINPEMLNKVLYRLGVAGQWRFVDVLGLEEESLGSVPAPACALLLLFPLTAQHENFRKKQIEELKGQEVSPKVYFMKQTIGNSCGTIGLIHAVANNQDKLGFEDGSVLKQFLSETEKMSPEDRAKCFEKNEAIQAAHDAVAQEGQCRVDDKVNFHFILFNNVDGHLYELDGRMPFPVNHGASSEDTLLKDAAKVCREFTEREQGEVRFSAVALCKAA

Whole chain analysis

Help Knotoid data interpretation Full screen

Subchain analysis

Knotoid cutoff: 0.5

Knotoid matrix content: 1

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

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

JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__546974268338501__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

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AppletRegistry.checkIn(jmolApplet0__546974268338501__)

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setting document base to "https://knotprot.cent.uw.edu.pl/view/3IFW/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:jmolApplet0 (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

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script 1 started

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Viewer cachePut cache://localLOAD_/static/knot_data/3ifw/A/3ifw_A.pdb.gz

Viewer cachePut https://knotprot.cent.uw.edu.pl/static/knot_data/3ifw/A/3ifw_A.pdb.gz

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FileManager.getAtomSetCollectionFromFile(/static/knot_data/3ifw/A/3ifw_A.pdb.gz)

The Resolver thinks Pdb

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

Time for openFile(/static/knot_data/3ifw/A/3ifw_A.pdb.gz): 247 ms

reading 223 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

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

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223 atoms created

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

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FileManager.getAtomSetCollectionFromFile(/static/knot_data/3ifw/A/3ifw_A.pdb.gz)

The Resolver thinks Pdb

Time for openFile(/static/knot_data/3ifw/A/3ifw_A.pdb.gz): 15 ms

reading 223 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

223 atoms created

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

Time for creating model: 15 ms

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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	5.2m	4-220	217	1-3, 221-223			3	3	knot
view details	2.1m	6-163	158	1-5	171-223	164-170	5	53	slipknot
view details	3.1m	4-170	167	1-3	174-223	171-173	3	50	slipknot
view details	2.1m	5-179	175	1-4	187-223	180-186	4	37	slipknot
view details	3.1m	8-185	178	1-7	191-223	186-190	7	33	slipknot
view details	2.1m	8-190	183	1-7	193-223	191-192	7	31	slipknot
view details	3.1m	5-192	188	1-4	210-223	193-209	4	14	slipknot
view details	2.1m	8-203	196	1-7	215-223	204-214	7	9	slipknot
view details	3.1m	5-214	210	1-4	218-223	215-217	4	6	slipknot
view details	2.1m	7-200	194		1-4, 203-223	5-6, 201-202	4	21	slipknot

sequence length	223
structure length	223
publication title	Ubiquitin vinyl methyl ester binding orients the misaligned active site of the ubiquitin hydrolase UCHL1 into productive conformation. pubmed doi rcsb
molecule tags	Hydrolase/hydrolase inhibitor
molecule keywords	Ubiquitin carboxyl-terminal hydrolase isozyme L1
source organism	Homo sapiens
total genus	Genus: 69
ec nomenclature	ec 3.4.19.12: Ubiquitinyl hydrolase 1.
pdb deposition date	2009-07-26
KnotProt deposition date	2014-07-31

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF01088	Peptidase_C12	Ubiquitin carboxyl-terminal hydrolase, family 1

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

cath code	Class	Architecture	Topology	Homology	Domain
3.40.532.10	Alpha Beta	3-Layer(aba) Sandwich	Ubiquitin C-terminal Hydrolase UCH-l3	Ubiquitin C-terminal Hydrolase Uch-l3	3ifwA00

1XD3A 3RISA 3KVFA 3IRTA 3RIIA 4DM9A 3IFWA 2ETLA 2LENA 1CMXA 1UCHA 3IHRA 3A7SA 3KW5A
chains in the KnotProt database with same CATH superfamily

1XD3A 3RISA 3KVFA 3IRTA 3RIIA 4DM9A 3IFWA 2ETLA 2LENA 1CMXA 1UCHA 3IHRA 3A7SA 3KW5A
chains in the KnotProt database with same CATH topology

1XD3A 3RISA 3KVFA 3IRTA 3RIIA 4DM9A 3IFWA 2ETLA 2LENA 1CMXA 1UCHA 3IHRA 3A7SA 3KW5A
chains in the KnotProt database with same CATH homology

#chains in the KnotProt database with same CATH superfamily
 1XD3 A;  3RIS A;  3KVF A;  3IRT A;  3RII A;  4DM9 A;  3IFW A;  2ETL A;  2LEN A;  1CMX A;  1UCH A;  3IHR A;  3A7S A;  3KW5 A; 
#chains in the KnotProt database with same CATH topology
 1XD3 A;  3RIS A;  3KVF A;  3IRT A;  3RII A;  4DM9 A;  3IFW A;  2ETL A;  2LEN A;  1CMX A;  1UCH A;  3IHR A;  3A7S A;  3KW5 A; 
#chains in the KnotProt database with same CATH homology
 1XD3 A;  3RIS A;  3KVF A;  3IRT A;  3RII A;  4DM9 A;  3IFW A;  2ETL A;  2LEN A;  1CMX A;  1UCH A;  3IHR A;  3A7S A;  3KW5 A;

2ETLA 2LENA 3IRTA 3KVFA 3KW5A 4DM9A 4JKJA
similar chains in the KnotProt database (40% sequence similarity)

7ZM0A 8DY8A
similar chains in the pdb database (40% sequence similarity)

#similar chains in the KnotProt database (40% sequence similarity)
2ETL A; 2LEN A; 3IRT A; 3KVF A; 3KW5 A; 4DM9 A; 4JKJ A; 
#similar chains, but unknotted

#similar chains in the pdb database (40% sequence similarity)
7ZM0 A; 8DY8 A;

3IFWA

Knot K -52 -31 -31

Chain Sequence

pfam database annotations

Knot K -5₂ -3₁ -3₁