4YFD: Crystal structure PTP delta Ig1-Fn2

Crystal structure PTP delta Ig1-Fn2 in complex with IL-1RAcP. Determined by X-ray diffraction at 3.25 Å resolution. Released 6 May 2015.

Method: X-ray diffraction
Resolution: 3.25 Å
Organism: Mus musculus
Chains: 2
Atoms: 6,505
Mol. weight: 94.83 kDa
Ligands: NAG
Released: 6 May 2015

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

Secondary structure: helices and β-sheets

4YFD contains 27 α-helices and 74 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: 21 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	29-35	7	9
β-strand	40-43	4	10
β-strand	48-57	10	9
α-helix	59-60	2
β-strand	61-66	6	10
β-strand	69-70	2	10
β-strand	76-80	5	9
β-strand	86-91	6	9
β-strand	101-109	9	10
β-strand	112-123	12	10
α-helix	125-127	3
α-helix	128-129	2
β-strand	134-137	4	11
β-strand	142-145	4	12
β-strand	150-157	8	11
α-helix	161-162	2
β-strand	163-168	6	12
β-strand	171-172	2	12
β-strand	182-186	5	11
α-helix	194	1
β-strand	195-201	7	11
α-helix	206-208	3
β-strand	210-218	9	12
β-strand	221-224	4	12
α-helix	225-227	3
β-strand	228-233	6	12
α-helix	234-236	3
α-helix	240	1
β-strand	241-247	7	13
α-helix	248-251	4
β-strand	252-253	2	14
β-strand	256	1	15
β-strand	258	1	15
β-strand	260-269	10	13
α-helix	271-272	2
β-strand	273-278	6	14
β-strand	281-282	2	14
β-strand	291	1	14
β-strand	293-298	6	13
β-strand	305-313	9	14
β-strand	316-325	10	14
α-helix	330-336	7
β-strand	337-341	5	16
β-strand	345-349	5	16
α-helix	357-358	2
β-strand	360-367	8	17
α-helix	373-374	2
β-strand	375-380	6	17
β-strand	384-388	5	16
α-helix	390-391	2
β-strand	395-403	9	17
β-strand	408-411	4	17
α-helix	412-414	3
β-strand	415-418	4	17
α-helix	419-421	3
α-helix	427-428	2
β-strand	429-435	7	18
β-strand	441-446	6	18
β-strand	457-463	7	19
α-helix	470-472	3
β-strand	474-479	6	19
β-strand	483-486	4	18
α-helix	489-490	2
β-strand	494-502	9	19
β-strand	507	1	19
α-helix	509-513	5
β-strand	514-517	4	19

Chain B: 6 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	1
β-strand	35-38	4	1
β-strand	43-46	4	2
α-helix	47	1
α-helix	48-50	3
α-helix	58-62	5
β-strand	67-74	8	1
β-strand	81-82	2	1
α-helix	88-90	3
β-strand	92-95	4	2
β-strand	98-101	4	2
α-helix	106-108	3
β-strand	110-117	8	1
β-strand	123-132	10	1
β-strand	134	1	3
β-strand	140	1	3
β-strand	146-150	5	4
β-strand	156-159	4	5
β-strand	174-179	6	4
β-strand	182-183	2	4
β-strand	190-192	3	5
β-strand	196-199	4	5
β-strand	208-218	11	4
β-strand	221-234	14	4
β-strand	244-245	2	6
β-strand	267-270	4	6
β-strand	279-283	5	7
β-strand	296-299	4	8
β-strand	302-304	3	6
β-strand	310-313	4	6
β-strand	315-318	4	8
α-helix	323-327	5
β-strand	331-335	5	7
β-strand	339-343	5	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-1 receptor accessory protein	B	protein	339	Mus musculus	Q61730 (AlphaFold model)
Receptor-type tyrosine-protein phosphatase delta	A	protein	491	Mus musculus	Q64487 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>4YFD_1 Interleukin-1 receptor accessory protein (chains B)
SERCDDWGLDTMRQIQVFEDEPARIKCPLFEHFLKYNYSTAHSSGLTLIWYWTRQDRDLE
EPINFRLPENRISKEKDVLWFRPTLLNDTGNYTCMLRNTTYCSKVAFPLEVVQKDSCFNS
AMRFPVHKMYIEHGIHKITCPNVDGYFPSSVKPSVTWYKGCTEIVDFHNVLPEGMNLSFF
IPLVSNNGNYTCVVTYPENGRLFHLTRTVTVKVVGSPKDALPPQIYSPNDRVVYEKEPGE
ELVIPCKVYFSFIMDSHNEVWWTIDGKKPDDVTVDITINESVSYSSTEDETRTQILSIKK
VTPEDLRRNYVCHARNTKGEAEQAAKVKQKVAAHHHHHH

Sequence of entity 2 (A), FASTA

>4YFD_2 Receptor-type tyrosine-protein phosphatase delta (chains A)
ETPPRFTRTPVDQTGVSGGVASFICQATGDPRPKIVWNKKGKKVSNQRFEVIEFDDGSGS
VLRIQPLRTPRDEAIYECVASNNVGEISVSTRLTVLREDQIPRGFPTIDMGPQLKVVERT
RTATMLCAASGNPDPEITWFKDFLPVDTSNNNGRIKQLRSESIGGTPIRGALQIEQSEES
DQGKYECVATNSAGTRYSAPANLYVRELREVRRVPPRFSIPPTNHEIMPGGSVNITCVAV
GSPMPYVKWMLGAEDLTPEDDMPIGRNVLELNDVRQSANYTCVAMSTLGVIEAIAQITVK
ALPKPPGTPVVTESTATSITLTWDSGNPEPVSYYIIQHKPKNSEEPYKEIDGIATTRYSV
AGLSPYSDYEFRVVAVNNIGRGPASEPVLTQTSEQAPSSAPRDVQARMLSSTTILVQWKE
PEEPNGQIQGYRVYYTMDPTQHVNNWMKHNVADSQITTIGNLVPQKTYSVKVLAFTSIGD
GPLSSDIQVIT

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7

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 Q61730 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VI4 2.79 Å, IL-33/ST2/IL-1RAcP ternary complex structure

Browse structure collections

About this viewer

MolViewer shows 4YFD directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.