4YH7: PTPdelta ectodomain

Crystal structure of PTPdelta ectodomain in complex with IL1RAPL1. Determined by X-ray diffraction at 4.4 Å resolution. Released 6 May 2015.

Method: X-ray diffraction
Resolution: 4.4 Å
Organism: Mus musculus
Chains: 2
Atoms: 7,240
Mol. weight: 135.15 kDa
Ligands: NAG
Released: 6 May 2015

Explore 4YH7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4YH7 contains 21 α-helices and 85 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, 56 β-strands

Element	Residues	Length	Sheet
β-strand	32-35	4	1
β-strand	40-43	4	2
β-strand	48-52	5	3
β-strand	53-55	3	1
α-helix	59-60	2
β-strand	61-66	6	2
β-strand	69-70	2	2
β-strand	73	1	3
β-strand	76-80	5	3
β-strand	87-91	5	3
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	4
β-strand	142-145	4	5
β-strand	150-157	8	4
α-helix	161-162	2
β-strand	163-168	6	5
β-strand	171-172	2	5
β-strand	182-186	5	4
α-helix	194	1
β-strand	195-201	7	4
α-helix	206-208	3
β-strand	210-218	9	5
β-strand	221-224	4	5
β-strand	228-233	6	5
β-strand	244-247	4	6
β-strand	252-253	2	7
β-strand	260-267	8	6
α-helix	271-272	2
β-strand	273-277	5	7
β-strand	282	1	7
β-strand	291	1	7
β-strand	293-298	6	6
β-strand	305-312	8	7
β-strand	317-318	2	7
β-strand	321-325	5	7
α-helix	330-333	4
β-strand	334-341	8	8
β-strand	346-351	6	8
β-strand	360-366	7	9
α-helix	373-374	2
β-strand	375-380	6	9
β-strand	384-387	4	8
α-helix	390-391	2
β-strand	395-403	9	9
β-strand	408	1	9
α-helix	410-414	5
β-strand	415-418	4	9
α-helix	427-428	2
β-strand	429-435	7	10
β-strand	441-446	6	10
β-strand	457-460	4	11
α-helix	470-472	3
β-strand	478	1	11
β-strand	483-486	4	10
α-helix	489-490	2
β-strand	494	1	12
β-strand	497-502	6	11
β-strand	507-514	8	11
β-strand	517	1	12
β-strand	527-532	6	13
β-strand	538-544	7	13
β-strand	553-561	9	14
β-strand	567-571	5	14
β-strand	576-580	5	13
β-strand	587-595	9	14
β-strand	600-603	4	14
β-strand	607-610	4	14

Chain B: 7 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	32-36	5	15
β-strand	41-44	4	15
β-strand	49-52	4	16
α-helix	54-56	3
α-helix	64-69	6
β-strand	73-79	7	15
α-helix	85-86	2
β-strand	87	1	15
β-strand	97	1	16
β-strand	102-105	4	16
α-helix	110-112	3
β-strand	114-121	8	15
β-strand	126-136	11	15
β-strand	150-155	6	17
β-strand	160-162	3	18
β-strand	182-183	2	17
β-strand	186	1	17
β-strand	194-196	3	18
β-strand	201-203	3	18
α-helix	208-210	3
β-strand	212-220	9	17
β-strand	223-234	12	17
β-strand	243-246	4	19
β-strand	253-256	4	20
β-strand	263-271	9	19
β-strand	274	1	21
β-strand	276	1	21
α-helix	277-279	3
β-strand	280-285	6	20
β-strand	288-289	2	20
α-helix	290-293	4
β-strand	298-300	3	19
β-strand	304-309	6	19
β-strand	312-321	10	19
β-strand	330-338	9	20
β-strand	341-350	10	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor-type tyrosine-protein phosphatase delta	A	protein	841	Mus musculus	Q64487 (AlphaFold model)
Interleukin-1 receptor accessory protein-like 1	B	protein	348	Mus musculus	P59823 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4YH7_1 Receptor-type tyrosine-protein phosphatase delta (chains A)
ETPPRFTRTPVDQTGVSGGVASFICQATGDPRPKIVWNKKGKKVSNQRFEVIEFDDGSGS
VLRIQPLRTPRDEAIYECVASNNVGEISVSTRLTVLREDQIPRGFPTIDMGPQLKVVERT
RTATMLCAASGNPDPEITWFKDFLPVDTSNNNGRIKQLRSESIGGTPIRGALQIEQSEES
DQGKYECVATNSAGTRYSAPANLYVRELREVRRVPPRFSIPPTNHEIMPGGSVNITCVAV
GSPMPYVKWMLGAEDLTPEDDMPIGRNVLELNDVRQSANYTCVAMSTLGVIEAIAQITVK
ALPKPPGTPVVTESTATSITLTWDSGNPEPVSYYIIQHKPKNSEEPYKEIDGIATTRYSV
AGLSPYSDYEFRVVAVNNIGRGPASEPVLTQTSEQAPSSAPRDVQARMLSSTTILVQWKE
PEEPNGQIQGYRVYYTMDPTQHVNNWMKHNVADSQITTIGNLVPQKTYSVKVLAFTSIGD
GPLSSDIQVITQTGVPGQPLNFKAEPESETSILLSWTPPRSDTIASYELVYRDGDQGEEQ
RITIEPGTSYRLQGLKPNSLYYFRLSARSPQGLGASTAEISARTMQSMFAKNFHVKAVMK
TSVLLSWEIPENYNSAMPFKILYDDGKMVEEVDGRATQKLIVNLKPEKSYSFVLTNRGNS
AGGLQHRVTAKTAPDVLRTKPAFIGKTNLDGMITVQLPDVPANENIKGYYIIIVPLKKSR
GKFIKPWESPDEMELDELLKEISRKRRSIRYGREVELKPYIAAHFDVLPTEFTLGDDKHY
GGFTNKQLQSGQEYVFFVLAVMDHAESKMYATSPYSDPVVSMDLDPQPITDEEEKHHHHH
H

Sequence of entity 2 (B), FASTA

>4YH7_2 Interleukin-1 receptor accessory protein-like 1 (chains B)
AQPAARDLKVVTKRGSADGCTDWSVDIKKYQVLVGEPVRIKCALFYGYIRTNYSLAQSAG
LSLMWYKSSGPGDFEEPIAFDGSRMSKEEDSIWFRPTLLQDSGLYACVIRNSTYCMKVSI
SLTVGENDTGLCYNSKMKYFEKAELSKSKEISCRDIEDFLLPTREPEILWYKECRTKAWR
PSIVFKRDTLLIKEVKEDDIGNYTCELKYGGFVVRRTTELTVTAPLTDKPPKLLYPMESK
LTVQETQLGGSANLTCRAFFGYSGDVSPLIYWMKGEKFIEDLDENRVWESDIRILKEHLG
EQEVSISLIVDSVEEGDLGNYSCYVENGNGRRHASVLLHKRKHHHHHH

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 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
4Y61 3.36 Å, Crystal structure of the complex between Slitrk2 LRR1 and PTP delta Ig1-Fn1
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

Browse structure collections

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