2YD8: Receptor-type tyrosine-protein phosphatase F

Crystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine Phosphatase LAR in complex with sucrose octasulphate. Determined by X-ray diffraction at 2.05 Å resolution. Released 13 Apr 2011.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: HOMO SAPIENS
Chains: 1
Atoms: 1,630
Mol. weight: 23.88 kDa
Ligands: YYJ
Released: 13 Apr 2011

Explore 2YD8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2YD8 contains 8 α-helices and 20 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	31-37	7	1
β-strand	42-45	4	2
β-strand	50-59	10	1
β-strand	63-68	6	2
β-strand	71-72	2	2
α-helix	73-74	2
β-strand	79-83	5	1
α-helix	84-86	3
β-strand	88-93	6	1
α-helix	98-101	4
β-strand	103-111	9	2
β-strand	114-125	12	2
α-helix	127-129	3
β-strand	136-139	4	3
β-strand	144-147	4	4
β-strand	152-154	3	5
β-strand	157-159	3	3
α-helix	163-164	2
β-strand	165-170	6	4
β-strand	173-174	2	4
α-helix	177-179	3
β-strand	184-186	3	5
β-strand	192-194	3	5
α-helix	199-201	3
β-strand	203-211	9	4
β-strand	214-217	4	4
α-helix	218-220	3
β-strand	221-226	6	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor-type tyrosine-protein phosphatase F	A	protein	214	HOMO SAPIENS	P10586 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2YD8_1 RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE F (chains A)
ETGDSKPVFIKVPEDQTGLSGGVASFVCQATGEPKPRITWMKKGKKVSSQRFEVIEFDDG
AGSVLRIQPLRVQRDEAIYECTATNSLGEINTSAKLSVLEEEQLPPGFPSIDMGPQLKVV
EKARTATMLCAAGGNPDPEISWFKDFLPVDPATSNGRIKQLRSGALQIESSEESDQGKYE
CVATNSAGTRYSAPANLYVRVRRVAGTKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
YYJ	1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose	C6 H12 O18 S4	1

Primary citation

Proteoglycan-Specific Molecular Switch for Rptp Sigma Clustering and Neuronal Extension. Coles, C.H., Shen, Y., Tenney, A.P. et al. Science (2011) 332:484. DOI 10.1126/SCIENCE.1200840 · PubMed

Other PDB entries of the same protein (UniProt P10586 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4N5U 1.46 Å, Crystal structure of the 4th FN3 domain of human Protein Tyrosine phosphatase, receptor…
6TPU 1.55 Å, Crystal structures of FNIII domain three and four of the human leucocyte common…
6TPV 1.8 Å, Crystal structures of FNIII domain one and two of the human leucocyte common…
1LAR 2.0 Å, Crystal structure of the tandem phosphatase domains of rptp lar
2YD5 2.2 Å, Crystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine…
6KR4 2.85 Å, Crystal structure of the liprin-alpha3_SAM123/LAR_D1D2 complex
6TPW 2.9 Å, Crystal structures of FNIII domain one through four of the human leucocyte common…
6TPT 3.2 Å, Crystal structures of FNIII domain three and four of the human leucocyte common…
2DJU Solution structures of the fn3 domain of human receptor-type tyrosine-protein…
2DN7 Solution structures of the 6th fn3 domain of human receptor-type tyrosine-protein…
2EDX Solution structures of the fn3 domain of human receptor-type tyrosine-protein…
2EDY Solution structures of the fn3 domain of human receptor-type tyrosine-protein…

Browse structure collections

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