1V6Z | KnotProt

1V6ZA

Crystal structure of tt1573 from thermus thermophilus

Image from the <span class='capital'>rcsb pdb</span> (www.rcsb.org)

Warning

Chain breaks within knotoid 3₁ (displayed as a gray area on the plot and as '-' on the sequence). The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.

Genus: 68

Knot K +3₁

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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				+3₁	156-200	45	1-155, 201-227			155	27	knot

Chain Sequence

RPHRAFSPGLTGVLPLRETRHLVEVLRARVGDRFTVFDGEREALAEVVDLGPPLRYRVLEERRPEREVGVEVVLYVALLKGDKLAEVVRAATELGATRIQPLVTRHSVPKEMGEGKLRRLRAVALEAAKQSGRVVVPEVLPPIPLKAVPQVAQGLVAHVGATARVREVLDPEKPLALAVGPEGGFAEEEVALLEARGFTPVSLGRRILRAETAALALLALCTAGEGR

Whole chain analysis

Help Knotoid data interpretation Full screen

Subchain analysis

Knotoid cutoff: 0.5

Knotoid matrix content: 1

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The Resolver thinks Pdb

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Time for openFile(/static/knot_data/1v6z/A/1v6z_A.pdb.gz): 565 ms

reading 227 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

227 atoms created

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

Time for creating model: 20 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	3.1	156-201	46	1-155, 202-227			155	26	knot
view details	2.1	153-198	46	1-152	204-227	199-203	152	24	slipknot
view details	2.1	157-206	50		1-155, 215-227	156-156, 207-214	155	13	slipknot
view details	2.1	157-214	58		1-155, 217-227	156-156, 215-216	155	11	slipknot
view details	2.1	157-217	61	218-227	1-155	156-156	155	9	slipknot

sequence length	227
structure length	227
publication title	Crystal structure of TT1573 from Thermus thermophilus rcsb
molecule tags	Transferase
molecule keywords	hypothetical protein TTHA0657
total genus	Genus: 68
ec nomenclature
pdb deposition date	2003-12-05
KnotProt deposition date	2014-07-31

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF04452	Methyltrans_RNA	RNA methyltransferase

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

cath code	Class	Architecture	Topology	Homology	Domain
2.40.240.20	Mainly Beta	Beta Barrel	Ribosomal Protein L25; Chain P	Hypothetical PUA domain-like; domain 1	1v6zA01
3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	Alpha/beta knot	1v6zA02

3DCMX 4CNGB 1X7PA 1VHKA 1MXIA 2O3AA 2YY8A 4E8BA 2CX8A 1NS5A 4H3YA 4IG6A 1X7OA 3IEFA 3ILKA 1UAKA 2QMMA 3N4KA 1K3RA 4FAKA 1O6DA 4CNFB 2HA8A 1NXZA 1VHYA 3AXZA 1ZJRA 4CNEB 3IC6A 3NK6A 3L8UA 3ONPA 3NK7A 3AI9X 3KY7A 1UALA 1UAMA 3AIAA 1GZ0A 3N4JA 4H3ZA 1J85A 3GYQA 1V6ZA 1P9PA 2Z0YA 1V2XA 2I6DA 2QWVA 3KTYA 3KNUA 3QUVA 3E5YA 1VH0A 1TO0A 3KW2A 1UAJA
chains in the KnotProt database with same CATH superfamily

#chains in the KnotProt database with same CATH superfamily
 3DCM X;  4CNG B;  1X7P A;  1VHK A;  1MXI A;  2O3A A;  2YY8 A;  4E8B A;  2CX8 A;  1NS5 A;  4H3Y A;  4IG6 A;  1X7O A;  3IEF A;  3ILK A;  1UAK A;  2QMM A;  3N4K A;  1K3R A;  4FAK A;  1O6D A;  4CNF B;  2HA8 A;  1NXZ A;  1VHY A;  3AXZ A;  1ZJR A;  4CNE B;  3IC6 A;  3NK6 A;  3L8U A;  3ONP A;  3NK7 A;  3AI9 X;  3KY7 A;  1UAL A;  1UAM A;  3AIA A;  1GZ0 A;  3N4J A;  4H3Z A;  1J85 A;  3GYQ A;  1V6Z A;  1P9P A;  2Z0Y A;  1V2X A;  2I6D A;  2QWV A;  3KTY A;  3KNU A;  3QUV A;  3E5Y A;  1VH0 A;  1TO0 A;  3KW2 A;  1UAJ A; 
#chains in the KnotProt database with same CATH topology
 3DCM X;  4CNG B;  1X7P A;  1VHK A;  1MXI A;  2O3A A;  2YY8 A;  4E8B A;  2CX8 A;  1NS5 A;  4H3Y A;  4IG6 A;  1X7O A;  3IEF A;  3ILK A;  1UAK A;  2QMM A;  3N4K A;  1K3R A;  4FAK A;  1O6D A;  4CNF B;  2HA8 A;  1NXZ A;  1VHY A;  3AXZ A;  1ZJR A;  4CNE B;  3IC6 A;  3NK6 A;  3L8U A;  3ONP A;  3NK7 A;  3AI9 X;  3KY7 A;  1UAL A;  1UAM A;  3AIA A;  1GZ0 A;  3N4J A;  4H3Z A;  1J85 A;  3GYQ A;  1V6Z A;  1P9P A;  2Z0Y A;  1V2X A;  2I6D A;  2QWV A;  3KTY A;  3KNU A;  3QUV A;  3E5Y A;  1VH0 A;  1TO0 A;  3KW2 A;  1UAJ A; 
#chains in the KnotProt database with same CATH homology
 3DCM X;  4CNG B;  1X7P A;  1VHK A;  1MXI A;  2O3A A;  2YY8 A;  4E8B A;  2CX8 A;  1NS5 A;  4H3Y A;  4IG6 A;  1X7O A;  3IEF A;  3ILK A;  1UAK A;  2QMM A;  3N4K A;  1K3R A;  4FAK A;  1O6D A;  4CNF B;  2HA8 A;  1NXZ A;  1VHY A;  3AXZ A;  1ZJR A;  4CNE B;  3IC6 A;  3NK6 A;  3L8U A;  3ONP A;  3NK7 A;  3AI9 X;  3KY7 A;  1UAL A;  1UAM A;  3AIA A;  1GZ0 A;  3N4J A;  4H3Z A;  1J85 A;  3GYQ A;  1V6Z A;  1P9P A;  2Z0Y A;  1V2X A;  2I6D A;  2QWV A;  3KTY A;  3KNU A;  3QUV A;  3E5Y A;  1VH0 A;  1TO0 A;  3KW2 A;  1UAJ A;

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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)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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How to cite

KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling

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1V6ZA

Knot K +31

Chain Sequence

pfam database annotations

Knot K +3₁