4Y61: Receptor-type tyrosine-protein phosphatase delta

Crystal structure of the complex between Slitrk2 LRR1 and PTP delta Ig1-Fn1. Determined by X-ray diffraction at 3.36 Å resolution. Released 3 Jun 2015.

Method: X-ray diffraction
Resolution: 3.36 Å
Organism: Mus musculus
Chains: 2
Atoms: 4,947
Mol. weight: 75.79 kDa
Ligands: NAG
Released: 3 Jun 2015

Explore 4Y61 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Y61 contains 21 α-helices and 53 β-strands across 2 chains. 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: 14 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	29-35	7	1
β-strand	40-43	4	2
β-strand	48-57	10	1
α-helix	59-60	2
β-strand	61-66	6	2
β-strand	69-70	2	2
β-strand	76-80	5	1
β-strand	86-91	6	1
β-strand	101-109	9	2
β-strand	112-123	12	2
α-helix	125-127	3
α-helix	128-129	2
β-strand	134-137	4	3
β-strand	142-145	4	4
β-strand	150-157	8	3
α-helix	161-162	2
β-strand	163-168	6	4
β-strand	171-172	2	4
α-helix	173-174	2
β-strand	182-185	4	3
α-helix	194	1
β-strand	195-201	7	3
α-helix	206-208	3
β-strand	210-218	9	4
β-strand	221-224	4	4
α-helix	225-227	3
β-strand	228-233	6	4
α-helix	234-237	4
β-strand	241-247	7	5
β-strand	252-254	3	6
β-strand	260-269	10	5
α-helix	271-272	2
β-strand	273-278	6	6
β-strand	281-282	2	6
β-strand	291	1	6
β-strand	293-298	6	5
β-strand	305-313	9	6
β-strand	316-326	11	6
α-helix	331-333	3
β-strand	334-342	9	7
β-strand	345-351	7	7
α-helix	357-358	2
β-strand	360-366	7	8
α-helix	373-374	2
β-strand	375-380	6	8
β-strand	384-388	5	7
α-helix	390-391	2
β-strand	396-403	8	8
β-strand	408	1	8
β-strand	415-417	3	8

Chain B: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	34-37	4	9
β-strand	42-45	4	9
β-strand	65-68	4	9
β-strand	76-77	2	10
β-strand	88-92	5	9
β-strand	100-101	2	10
β-strand	114-116	3	9
β-strand	124-125	2	11
β-strand	138-140	3	9
β-strand	148-149	2	11
α-helix	151-154	4
β-strand	162-164	3	9
β-strand	185-187	3	9
α-helix	198-202	5
α-helix	203-204	2
β-strand	210-212	3	9
β-strand	218-219	2	12
α-helix	222-224	3
α-helix	225-233	9
β-strand	242	1	13
β-strand	243-245	3	12
α-helix	247-249	3
β-strand	253	1	13
α-helix	259-262	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor-type tyrosine-protein phosphatase delta	A	protein	398	Mus musculus	Q64487 (AlphaFold model)
SLIT and NTRK-like protein 2	B	protein	272	Mus musculus	Q810C0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4Y61_1 Receptor-type tyrosine-protein phosphatase delta (chains A)
ETPPRFTRTPVDQTGVSGGVASFICQATGDPRPKIVWNKKGKKVSNQRFEVIEFDDGSGS
VLRIQPLRTPRDEAIYECVASNNVGEISVSTRLTVLREDQIPRGFPTIDMGPQLKVVERT
RTATMLCAASGNPDPEITWFKDFLPVDTSNNNGRIKQLRSESIGGTPIRGALQIEQSEES
DQGKYECVATNSAGTRYSAPANLYVRELREVRRVPPRFSIPPTNHEIMPGGSVNITCVAV
GSPMPYVKWMLGAEDLTPEDDMPIGRNVLELNDVRQSANYTCVAMSTLGVIEAIAQITVK
ALPKPPGTPVVTESTATSITLTWDSGNPEPVSYYIIQHKPKNSEEPYKEIDGIATTRYSV
AGLSPYSDYEFRVVAVNNIGRGPASEPVLTQKHHHHHH

Sequence of entity 2 (B), FASTA

>4Y61_2 SLIT and NTRK-like protein 2 (chains B)
MLSGVWFLSVLTVAGILQTESRKTAKDICKIRCLCEEKENVLNINCENKGFTTVSLLQPP
QYRIYQLFLNGNLLTRLYPNEFVNYSNAVTLHLGNNGLQEIRPGAFSGLKTLKRLHLNNN
KLEVLREDTFLGLESLEYLQADYNYISTIEAGAFSKLNKLKVLILNDNLLLSLPSNVFRF
VLLTHLDLRGNRLKVMPFAGVLEHIGGIMEIQLEENPWNCTCDLLPLKAWLDTITVFVGE
IVCETPFRLHGKDVTQLTRQDLCPRKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Structure of Slitrk2-PTP delta complex reveals mechanisms for splicing-dependent trans-synaptic adhesion. Yamagata, A., Sato, Y., Goto-Ito, S. et al. Sci Rep (2015) 5:9686-9686. DOI 10.1038/srep09686 · PubMed

Other PDB entries of the same protein (UniProt Q64487 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KIP 1.91 Å, Crystal structure of PTPRD phosphatase domain in complex with Liprin-alpha3 tandem SAM…
4YFE 1.97 Å, Crystal structure of PTP delta Fn1-Fn2
5Y32 2.7 Å, Crystal structure of PTP delta Ig1-Ig2 in complex with IL1RAPL1
5XWU 3.16 Å, Crystal structure of PTPdelta Ig1-Ig3 in complex with SALM2 LRR-Ig
4YFD 3.25 Å, Crystal structure PTP delta Ig1-Fn2 in complex with IL-1RAcP
4YFG 3.49 Å, Crystal structure of PTP delta meA3/meB minus variant Ig1-Fn1
7CEG 3.85 Å, Crystal structure of the complex between mouse PTP delta and neuroligin-3
5XWT 4.18 Å, Crystal structure of PTPdelta Ig1-Fn1 in complex with SALM5 LRR-Ig
4YH7 4.4 Å, Crystal structure of PTPdelta ectodomain in complex with IL1RAPL1

Browse structure collections

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