5Y32: PTP delta Ig1-Ig2

Crystal structure of PTP delta Ig1-Ig2 in complex with IL1RAPL1. Determined by X-ray diffraction at 2.7 Å resolution. Released 16 Aug 2017.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Mus musculus
Chains: 2
Atoms: 4,428
Mol. weight: 75.48 kDa
Ligands: NAG
Released: 16 Aug 2017

Explore 5Y32 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Y32 contains 15 α-helices and 48 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: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	29-35	7	8
β-strand	40-43	4	9
β-strand	48-57	10	8
α-helix	59-60	2
β-strand	61-66	6	9
β-strand	69-70	2	9
α-helix	71	1
β-strand	76-80	5	8
β-strand	86-91	6	8
β-strand	101-108	8	9
β-strand	113-123	11	9
α-helix	128-129	2
β-strand	134-137	4	10
β-strand	142-145	4	11
β-strand	150-157	8	10
α-helix	161-162	2
β-strand	163-168	6	11
β-strand	171-172	2	11
α-helix	173	1
β-strand	182-186	5	10
α-helix	194	1
β-strand	195-201	7	10
α-helix	206-208	3
β-strand	210-218	9	11
β-strand	221-224	4	11
β-strand	228-233	6	11
α-helix	234-235	2

Chain B: 7 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	32-36	5	1
β-strand	41-44	4	1
β-strand	49-52	4	2
α-helix	54-57	4
α-helix	64-69	6
β-strand	73-79	7	1
β-strand	87-88	2	1
α-helix	89	1
β-strand	97	1	2
β-strand	102-105	4	2
α-helix	110-112	3
β-strand	114-121	8	1
β-strand	126-136	11	1
α-helix	138-139	2
β-strand	145	1	3
β-strand	148	1	3
β-strand	150-155	6	4
β-strand	160-163	4	5
β-strand	180-183	4	4
β-strand	186	1	4
β-strand	194-196	3	5
β-strand	200-203	4	5
α-helix	208-210	3
β-strand	212-220	9	4
β-strand	223-234	12	4
β-strand	243-246	4	6
β-strand	253-257	5	7
β-strand	263-271	9	6
α-helix	277-279	3
β-strand	280-285	6	7
β-strand	288-289	2	7
β-strand	298-300	3	6
β-strand	304-308	5	6
β-strand	313-321	9	6
β-strand	330-338	9	7
β-strand	341-351	11	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-1 receptor accessory protein-like 1	B	protein	346	Mus musculus	P59823 (AlphaFold model)
Receptor-type tyrosine-protein phosphatase delta	A	protein	305	Mus musculus	Q64487 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>5Y32_1 Interleukin-1 receptor accessory protein-like 1 (chains B)
PAARDLKVVTKRGSADGCTDWSVDIKKYQVLVGEPVRIKCALFYGYIRTNYSLAQSAGLS
LMWYKSSGPGDFEEPIAFDGSRMSKEEDSIWFRPTLLQDSGLYACVIRNSTYCMKVSISL
TVGENDTGLCYNSKMKYFEKAELSKSKEISCRDIEDFLLPTREPEILWYKECRTKAWRPS
IVFKRDTLLIKEVKEDDIGNYTCELKYGGFVVRRTTELTVTAPLTDKPPKLLYPMESKLT
VQETQLGGSANLTCRAFFGYSGDVSPLIYWMKGEKFIEDLDENRVWESDIRILKEHLGEQ
EVSISLIVDSVEEGDLGNYSCYVENGNGRRHASVLLHKRKHHHHHH

Sequence of entity 2 (A), FASTA

>5Y32_2 Receptor-type tyrosine-protein phosphatase delta (chains A)
ETPPRFTRTPVDQTGVSGGVASFICQATGDPRPKIVWNKKGKKVSNQRFEVIEFDDGSGS
VLRIQPLRTPRDEAIYECVASNNVGEISVSTRLTVLREDQIPRGFPTIDMGPQLKVVERT
RTATMLCAASGNPDPEITWFKDFLPVDTSNNNGRIKQLRSESIGGTPIRGALQIEQSEES
DQGKYECVATNSAGTRYSAPANLYVRELREVRRVPPRFSIPPTNHEIMPGGSVNITCVAV
GSPMPYVKWMLGAEDLTPEDDMPIGRNVLELNDVRQSANYTCVAMSTLGVIEAIAQITKH
HHHHH

Ligands and cofactors

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

Primary citation

Mechanisms of splicing-dependent trans-synaptic adhesion by PTP delta-IL1RAPL1/IL-1RAcP for synaptic differentiation. Yamagata, A., Yoshida, T., Sato, Y. et al. Nat Commun (2015) 6:6926-6926. DOI 10.1038/ncomms7926 · PubMed

Other PDB entries of the same protein (UniProt P59823 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4YH6 3.0 Å, Crystal structure of IL1RAPL1 ectodomain
4YH7 4.4 Å, Crystal structure of PTPdelta ectodomain in complex with IL1RAPL1

Browse structure collections

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