4YFG: PTP delta meA3/meB minus variant Ig1-Fn1

Crystal structure of PTP delta meA3/meB minus variant Ig1-Fn1. Determined by X-ray diffraction at 3.49 Å resolution. Released 6 May 2015.

Method: X-ray diffraction
Resolution: 3.49 Å
Organism: Mus musculus
Chains: 2
Atoms: 7,468
Mol. weight: 108.4 kDa
Ligands: NAG
Released: 6 May 2015

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

Secondary structure: helices and β-sheets

4YFG contains 34 α-helices and 92 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: 16 helices, 47 β-strands

Element	Residues	Length	Sheet
β-strand	29-35	7	12
β-strand	40-43	4	13
β-strand	48-57	10	12
α-helix	59-60	2
β-strand	61-66	6	13
β-strand	70	1	13
β-strand	76-80	5	12
β-strand	86-91	6	12
β-strand	101-109	9	13
β-strand	112-123	12	13
α-helix	128-129	2
β-strand	134-137	4	14
β-strand	142-145	4	15
β-strand	150-153	4	16
β-strand	155-157	3	14
α-helix	161-162	2
β-strand	163-168	6	15
β-strand	171-172	2	15
α-helix	173	1
β-strand	182-185	4	16
β-strand	192-195	4	16
α-helix	200-202	3
β-strand	204-212	9	15
β-strand	215-218	4	15
β-strand	222-227	6	15
β-strand	234-237	4	17
α-helix	238-241	4
β-strand	242-244	3	18
β-strand	246	1	19
β-strand	248	1	19
β-strand	250-257	8	17
β-strand	263-267	5	18
β-strand	272	1	18
β-strand	281	1	18
β-strand	283-288	6	17
β-strand	295-303	9	18
β-strand	306-316	11	18
α-helix	319-326	8
β-strand	327-331	5	20
β-strand	336-339	4	20
α-helix	347-348	2
β-strand	350-357	8	21
α-helix	363-364	2
β-strand	365-370	6	21
β-strand	374-377	4	20
α-helix	380-381	2
β-strand	385-393	9	21
β-strand	398	1	21
α-helix	400-404	5
β-strand	405-408	4	21
α-helix	409-411	3
α-helix	417-418	2
β-strand	419-425	7	22
β-strand	431-436	6	22
β-strand	447-453	7	23
α-helix	460-462	3
β-strand	464-469	6	23
β-strand	473-476	4	22
α-helix	479-480	2
β-strand	484-492	9	23
β-strand	497	1	23
α-helix	499-503	5
β-strand	504-507	4	23

Chain B: 18 helices, 45 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	3
β-strand	69-70	2	3
β-strand	77-80	4	1
β-strand	86-91	6	1
β-strand	102-109	8	3
β-strand	112-119	8	3
β-strand	120-123	4	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
α-helix	173	1
β-strand	182-187	6	4
β-strand	190-195	6	4
α-helix	200-202	3
β-strand	204-212	9	5
β-strand	215-218	4	5
β-strand	222-227	6	5
α-helix	228-230	3
β-strand	234-237	4	6
α-helix	238-241	4
β-strand	242-243	2	7
β-strand	250-257	8	6
β-strand	263-267	5	7
β-strand	272	1	7
α-helix	273	1
β-strand	281	1	7
β-strand	283-288	6	6
β-strand	295-303	9	7
β-strand	306-315	10	7
α-helix	320-326	7
β-strand	327-331	5	8
β-strand	336-339	4	8
β-strand	350-357	8	9
α-helix	363-364	2
β-strand	365-370	6	9
β-strand	374-377	4	8
α-helix	380-381	2
β-strand	385-393	9	9
β-strand	398	1	9
α-helix	400-404	5
β-strand	405-408	4	9
α-helix	409-411	3
α-helix	417-418	2
β-strand	419-425	7	10
β-strand	431-436	6	10
β-strand	447-453	7	11
α-helix	460-462	3
β-strand	464-469	6	11
β-strand	473-476	4	10
α-helix	479-480	2
β-strand	484-492	9	11
β-strand	497	1	11
α-helix	499-503	5
β-strand	504-507	4	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor-type tyrosine-protein phosphatase delta	A, B	protein	488	Mus musculus	Q64487 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4YFG_1 Receptor-type tyrosine-protein phosphatase delta (chains A, B)
ETPPRFTRTPVDQTGVSGGVASFICQATGDPRPKIVWNKKGKKVSNQRFEVIEFDDGSGS
VLRIQPLRTPRDEAIYECVASNNVGEISVSTRLTVLREDQIPRGFPTIDMGPQLKVVERT
RTATMLCAASGNPDPEITWFKDFLPVDTSNNNGRIKQLRSESIGALQIEQSEESDQGKYE
CVATNSAGTRYSAPANLYVRVRRVPPRFSIPPTNHEIMPGGSVNITCVAVGSPMPYVKWM
LGAEDLTPEDDMPIGRNVLELNDVRQSANYTCVAMSTLGVIEAIAQITVKALPKPPGTPV
VTESTATSITLTWDSGNPEPVSYYIIQHKPKNSEEPYKEIDGIATTRYSVAGLSPYSDYE
FRVVAVNNIGRGPASEPVLTQTSEQAPSSAPRDVQARMLSSTTILVQWKEPEEPNGQIQG
YRVYYTMDPTQHVNNWMKHNVADSQITTIGNLVPQKTYSVKVLAFTSIGDGPLSSDIQVI
TKHHHHHH

Ligands and cofactors

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

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
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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