3BDG | KnotProt

3BDGA

Crystal structure of wild-type/t155v mixed dimer of e. coli alkaline phosphatase

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

Warning

Chain breaks within knot 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 The broken part of the chain has been replaced by a straight segment, which may affect what knot types are detected - be careful with interpreting results.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: 159

Slipknot S +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	46-367	322	1-45	418-448	368-417	45	31	slipknot

Chain Sequence

PEMPVLENRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQDAVPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASI------ANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGHTGSQL--------RIAAYGPHAANVVGLTDQTDLFYTMKAALGLK

Whole chain analysis

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Subchain analysis

Knotoid cutoff: 0.5

Knotoid matrix content: 1

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Viewer cachePut cache://localLOAD_/static/knot_data/3bdg/A/3bdg_A.pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/static/knot_data/3bdg/A/3bdg_A.pdb.gz): 1069 ms

reading 434 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

434 atoms created

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

Time for creating model: 56 ms

Adding embedded #jmolscript: select ({0:433});backbone only;select *;

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	46-365	320	1-45	396-434	366-395	45	39	slipknot
view details	3.1	46-395	350	1-45	402-434	396-401	45	33	slipknot
view details	2.1	44-401	358	1-43	406-434	402-405	43	29	slipknot
view details	2.1	37-405	369		1-5, 407-434	6-36, 406-406	5	28	slipknot
view details	2.1	31-359	329		1-7, 366-434	8-30, 360-365	7	69	slipknot
view details	2.1	38-360	323		1-30, 366-434	31-37, 361-365	30	69	slipknot
view details	2.1	39-361	323		1-37, 366-434	38-38, 362-365	37	69	slipknot

sequence length	448
structure length	434
publication title	The Active-Site Trimetallic Cluster of Alkaline Phosphatase is Lost Upon Isosteric Mutation at the Mg2+-Coordinating Residue Threonine-155 rcsb
molecule tags	Hydrolase
molecule keywords	Alkaline phosphatase
source organism	Escherichia coli
missing residues	326-331, 403-410
total genus	Genus: 159
ec nomenclature	ec 3.1.3.1: Alkaline phosphatase.
pdb deposition date	2007-11-14
KnotProt deposition date	2014-07-31

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00245	Alk_phosphatase	Alkaline phosphatase

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

cath code	Class	Architecture	Topology	Homology	Domain
3.40.720.10	Alpha Beta	3-Layer(aba) Sandwich	Alkaline Phosphatase, subunit A	Alkaline Phosphatase, subunit A	3bdgA00

1ZEBA 1AJAA 1ALJA 2GLQA 3TWZA 1KH4A 1KH7A 1ANJA 2GA3A 1KHKA 3NVLA 3UN5A 3M7VA 1N2KA 1ELYA 1AUKA 1E1ZP 1O99A 3OT9A 1KH5A 3M8ZA 1HDHA 1URBA 3SZZA 1K7HA 1ELZA 2QZUA 1EI6A 1HJKA 1KHLA 1FSUA 3T01A 1E2SP 1ZEDA 1AJCA 1SHQA 3CMRA 1EQJA 1EW2A 3UN3A 3IGZB 1B8JA 2IFYA 3SZYA 1ED8A 1ANIA 2ANHA 1ZEFA 3UO0A 1KH9A 3TX0A 3MK2A 4FDIA 3M8YA 1ALIA 4FDJA 1E3CP 1EW9A 3UNYA 2G9YA 1ALKA 3ED4A 3DPCA 1ELXA 1EW8A 1O98A 1AJDA 1AJBA 3T02A 3T00A 1N2LA 3MK0A 1EJJA 1Y6VA 3BDFA 1URAA 1KHNA 1Y7AA 3M8WA 3MK1A 3UN2A 1E33P 1P49A 3DYCA 1HQAA 1ED9A 1SHNA 3BDGA 3BDHA 3IGYB 1KHJA 3BDGB
chains in the KnotProt database with same CATH superfamily

#chains in the KnotProt database with same CATH superfamily
 1ZEB A;  1AJA A;  1ALJ A;  2GLQ A;  3TWZ A;  1KH4 A;  1KH7 A;  1ANJ A;  2GA3 A;  1KHK A;  3NVL A;  3UN5 A;  3M7V A;  1N2K A;  1ELY A;  1AUK A;  1E1Z P;  1O99 A;  3OT9 A;  1KH5 A;  3M8Z A;  1HDH A;  1URB A;  3SZZ A;  1K7H A;  1ELZ A;  2QZU A;  1EI6 A;  1HJK A;  1KHL A;  1FSU A;  3T01 A;  1E2S P;  1ZED A;  1AJC A;  1SHQ A;  3CMR A;  1EQJ A;  1EW2 A;  3UN3 A;  3IGZ B;  1B8J A;  2IFY A;  3SZY A;  1ED8 A;  1ANI A;  2ANH A;  1ZEF A;  3UO0 A;  1KH9 A;  3TX0 A;  3MK2 A;  4FDI A;  3M8Y A;  1ALI A;  4FDJ A;  1E3C P;  1EW9 A;  3UNY A;  2G9Y A;  1ALK A;  3ED4 A;  3DPC A;  1ELX A;  1EW8 A;  1O98 A;  1AJD A;  1AJB A;  3T02 A;  3T00 A;  1N2L A;  3MK0 A;  1EJJ A;  1Y6V A;  3BDF A;  1URA A;  1KHN A;  1Y7A A;  3M8W A;  3MK1 A;  3UN2 A;  1E33 P;  1P49 A;  3DYC A;  1HQA A;  1ED9 A;  1SHN A;  3BDG A;  3BDH A;  3IGY B;  1KHJ A;  3BDG B; 
#chains in the KnotProt database with same CATH topology
 1ZEB A;  1AJA A;  1ALJ A;  2GLQ A;  3TWZ A;  1KH4 A;  1KH7 A;  1ANJ A;  2GA3 A;  1KHK A;  3NVL A;  3UN5 A;  3M7V A;  1N2K A;  1ELY A;  1AUK A;  1E1Z P;  1O99 A;  3OT9 A;  1KH5 A;  3M8Z A;  1HDH A;  1URB A;  3SZZ A;  1K7H A;  1ELZ A;  2QZU A;  1EI6 A;  1HJK A;  1KHL A;  1FSU A;  3T01 A;  1E2S P;  1ZED A;  1AJC A;  1SHQ A;  3CMR A;  1EQJ A;  1EW2 A;  3UN3 A;  3IGZ B;  1B8J A;  2IFY A;  3SZY A;  1ED8 A;  1ANI A;  2ANH A;  1ZEF A;  3UO0 A;  1KH9 A;  3TX0 A;  3MK2 A;  4FDI A;  3M8Y A;  1ALI A;  4FDJ A;  1E3C P;  1EW9 A;  3UNY A;  2G9Y A;  1ALK A;  3ED4 A;  3DPC A;  1ELX A;  1EW8 A;  1O98 A;  1AJD A;  1AJB A;  3T02 A;  3T00 A;  1N2L A;  3MK0 A;  1EJJ A;  1Y6V A;  3BDF A;  1URA A;  1KHN A;  1Y7A A;  3M8W A;  3MK1 A;  3UN2 A;  1E33 P;  1P49 A;  3DYC A;  1HQA A;  1ED9 A;  1SHN A;  3BDG A;  3BDH A;  3IGY B;  1KHJ A;  3BDG B; 
#chains in the KnotProt database with same CATH homology
 1ZEB A;  1AJA A;  1ALJ A;  2GLQ A;  3TWZ A;  1KH4 A;  1KH7 A;  1ANJ A;  2GA3 A;  1KHK A;  3NVL A;  3UN5 A;  3M7V A;  1N2K A;  1ELY A;  1AUK A;  1E1Z P;  1O99 A;  3OT9 A;  1KH5 A;  3M8Z A;  1HDH A;  1URB A;  3SZZ A;  1K7H A;  1ELZ A;  2QZU A;  1EI6 A;  1HJK A;  1KHL A;  1FSU A;  3T01 A;  1E2S P;  1ZED A;  1AJC A;  1SHQ A;  3CMR A;  1EQJ A;  1EW2 A;  3UN3 A;  3IGZ B;  1B8J A;  2IFY A;  3SZY A;  1ED8 A;  1ANI A;  2ANH A;  1ZEF A;  3UO0 A;  1KH9 A;  3TX0 A;  3MK2 A;  4FDI A;  3M8Y A;  1ALI A;  4FDJ A;  1E3C P;  1EW9 A;  3UNY A;  2G9Y A;  1ALK A;  3ED4 A;  3DPC A;  1ELX A;  1EW8 A;  1O98 A;  1AJD A;  1AJB A;  3T02 A;  3T00 A;  1N2L A;  3MK0 A;  1EJJ A;  1Y6V A;  3BDF A;  1URA A;  1KHN A;  1Y7A A;  3M8W A;  3MK1 A;  3UN2 A;  1E33 P;  1P49 A;  3DYC A;  1HQA A;  1ED9 A;  1SHN A;  3BDG A;  3BDH A;  3IGY B;  1KHJ A;  3BDG B;

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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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3BDGA

Slipknot S +31

Chain Sequence

pfam database annotations

Slipknot S +3₁