2YD7: Ptprd protein

Crystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine Phosphatase Delta. Determined by X-ray diffraction at 1.98 Å resolution. Released 13 Apr 2011.

Method: X-ray diffraction
Resolution: 1.98 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 3,234
Mol. weight: 47.25 kDa
Ligands: PO4
Released: 13 Apr 2011

Explore 2YD7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2YD7 contains 15 α-helices and 38 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, 19 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	1
β-strand	33-36	4	2
β-strand	41-50	10	1
α-helix	52-53	2
β-strand	54-59	6	2
β-strand	62-63	2	2
β-strand	69-73	5	1
β-strand	79-84	6	1
β-strand	94-102	9	2
β-strand	105-116	12	2
α-helix	118-120	3
β-strand	127-130	4	3
β-strand	135-137	3	4
α-helix	142	1
β-strand	143-150	8	3
α-helix	154-155	2
β-strand	156-161	6	4
β-strand	164-165	2	4
β-strand	175-180	6	3
β-strand	183-188	6	3
α-helix	193-195	3
β-strand	197-205	9	4
β-strand	208-211	4	4
α-helix	212-214	3
β-strand	215-219	5	4

Chain B: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	5
β-strand	33-36	4	2
β-strand	41-50	10	5
α-helix	52-53	2
β-strand	54-59	6	2
β-strand	62-63	2	2
β-strand	69-74	6	5
α-helix	75-77	3
β-strand	79-84	6	5
β-strand	94-101	8	2
β-strand	106-116	11	2
α-helix	118-120	3
α-helix	121-122	2
β-strand	127-130	4	6
β-strand	135-137	3	7
α-helix	142	1
β-strand	143-150	8	6
α-helix	154-155	2
β-strand	156-161	6	7
β-strand	164-165	2	7
α-helix	166-167	2
β-strand	175-180	6	6
β-strand	183-188	6	6
α-helix	193-195	3
β-strand	197-205	9	7
β-strand	208-211	4	7
α-helix	212-214	3
β-strand	215-219	5	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ptprd protein	A, B	protein	212	HOMO SAPIENS	P23468 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2YD7_1 PTPRD PROTEIN (chains A, B)
ETGETPPRFTRTPVDQTGVSGGVASFICQATGDPRPKIVWNKKGKKVSNQRFEVIEFDDG
SGSVLRIQPLRTPRDEAIYECVASNNVGEISVSTRLTVLREDQIPRGFPTIDMGPQLKVV
ERTRTATMLCAASGNPDPEITWFKDFLPVDTSNNNGRIKQLRSESIGALQIEQSEESDQG
KYECVATNSAGTRYSAPANLYVRGTKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	3

Primary citation

Proteoglycan-Specific Molecular Switch for Rptp Sigma Clustering and Neuronal Extension. Coles, C.H., Shen, Y., Tenney, A.P. et al. Science (2011) 332:484. DOI 10.1126/SCIENCE.1200840 · 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
4RCA 2.99 Å, Crystal structure of human PTPdelta and human Slitrk1 complex
5WY8 3.07 Å, Crystal structure of PTP delta Ig1-Ig3 in complex with IL1RAPL1 Ig1-Ig3
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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