5WY8: PTP delta Ig1-Ig3

Crystal structure of PTP delta Ig1-Ig3 in complex with IL1RAPL1 Ig1-Ig3. Determined by X-ray diffraction at 3.07 Å resolution. Released 22 Nov 2017.

Method: X-ray diffraction
Resolution: 3.07 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,081
Mol. weight: 72.77 kDa
Ligands: NAG, ZN
Released: 22 Nov 2017

Explore 5WY8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5WY8 contains 17 α-helices and 57 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: 6 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	25-28	4	1
β-strand	33-36	4	2
β-strand	41-45	5	3
β-strand	46-48	3	1
α-helix	52-53	2
β-strand	54-59	6	2
β-strand	62-63	2	2
β-strand	69-73	5	3
β-strand	80-84	5	3
β-strand	94-101	8	2
β-strand	106-116	11	2
β-strand	127-130	4	4
α-helix	132-134	3
β-strand	135-138	4	5
β-strand	143-150	8	4
β-strand	156-161	6	5
β-strand	164-165	2	5
β-strand	175-179	5	4
β-strand	188-194	7	4
α-helix	199-201	3
β-strand	203-210	8	5
β-strand	215-217	3	5
α-helix	218-220	3
β-strand	221-226	6	5
β-strand	234-240	7	6
α-helix	241-244	4
β-strand	245	1	7
β-strand	253-262	10	6
α-helix	264-265	2
β-strand	266-271	6	7
β-strand	274-275	2	7
β-strand	284	1	7
β-strand	286-291	6	6
β-strand	298-305	8	7
β-strand	310-317	8	7

Chain B: 11 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	32-34	3	8
β-strand	40-44	5	8
β-strand	49-52	4	9
α-helix	54	1
α-helix	55-59	5
α-helix	64-69	6
β-strand	73-79	7	8
α-helix	85-86	2
β-strand	87-88	2	8
β-strand	96-99	4	9
β-strand	102-105	4	9
α-helix	110-112	3
β-strand	114-121	8	8
β-strand	126-136	11	8
α-helix	137-139	3
β-strand	150-155	6	10
β-strand	160-163	4	11
α-helix	168-170	3
β-strand	180-183	4	10
β-strand	186	1	10
α-helix	189-191	3
β-strand	194	1	11
β-strand	197	1	11
β-strand	200-203	4	11
α-helix	208-210	3
β-strand	212-220	9	10
β-strand	223-234	12	10
α-helix	235-238	4
β-strand	243-246	4	12
α-helix	248	1
β-strand	253-254	2	13
β-strand	263-271	9	12
β-strand	280-285	6	13
β-strand	288	1	13
β-strand	298-300	3	12
β-strand	304-309	6	12
β-strand	312-321	10	12
β-strand	331-338	8	13
β-strand	341-348	8	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor-type tyrosine-protein phosphatase delta	A	protein	298	Homo sapiens	P23468 (AlphaFold model)
Interleukin-1 receptor accessory protein-like 1	B	protein	323	Homo sapiens	Q9NZN1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5WY8_1 Receptor-type tyrosine-protein phosphatase delta (chains A)
ETPPRFTRTPVDQTGVSGGVASFICQATGDPRPKIVWNKKGKKVSNQRFEVIEFDDGSGS
VLRIQPLRTPRDEAIYECVASNNVGEISVSTRLTVLREDQIPRGFPTIDMGPQLKVVERT
RTATMLCAASGNPDPEITWFKDFLPVDTSNNNGRIKQLRSESIGGTPIRGALQIEQSEES
DQGKYECVATNSAGTRYSAPANLYVRELREVRRVPPRFSIPPTNHEIMPGGSVNITCVAV
GSPMPYVKWMLGAEDLTPEDDMPIGRNVLELNDVRQSANYTCVAMSTLGVIEAIAQIT

Sequence of entity 2 (B), FASTA

>5WY8_2 Interleukin-1 receptor accessory protein-like 1 (chains B)
SADGCTDWSIDIKKYQVLVGEPVRIKCALFYGYIRTNYSLAQSAGLSLMWYKSSGPGDFE
EPIAFDGSRMSKEEDSIWFRPTLLQDSGLYACVIRNSTYCMKVSISLTVGENDTGLCYNS
KMKYFEKAELSKSKEISCRDIEDFLLPTREPEILWYKECRTKTWRPSIVFKRDTLLIREV
REDDIGNYTCELKYGGFVVRRTTELTVTAPLTDKPPKLLYPMESKLTIQETQLGDSANLT
CRAFFGYSGDVSPLIYWMKGEKFIEDLDENRVWESDIRILKEHLGEQEVSISLIVDSVEE
GDLGNYSCYVENGNGRRHASVLL

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
ZN	Zinc ion	Zn	3

Primary citation

LAR-RPTP Clustering Is Modulated by Competitive Binding between Synaptic Adhesion Partners and Heparan Sulfate. Won, S.Y., Kim, C.Y., Kim, D. et al. Front Mol Neurosci (2017) 10:327-327. DOI 10.3389/fnmol.2017.00327 · PubMed

Other PDB entries of the same protein (UniProt P23468 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2YD6 1.35 Å, Crystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine…
6X3A 1.77 Å, Crystal structure of the FN4-FN6 domains of human PTPRD
2YD7 1.98 Å, Crystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine…
4RCA 2.99 Å, Crystal structure of human PTPdelta and human Slitrk1 complex
5XNP 3.73 Å, Crystal structures of human SALM5 in complex with human PTPdelta
1X5Z Solution structure of the fibronectin type-III domain of human protein tyrosine…
2DLH Solution structure of the second fn3 domain of human receptor-type tyrosine-protein…

Browse structure collections

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