5XWU: PTPdelta Ig1-Ig3

Crystal structure of PTPdelta Ig1-Ig3 in complex with SALM2 LRR-Ig. Determined by X-ray diffraction at 3.16 Å resolution. Released 6 Jun 2018.

Method: X-ray diffraction
Resolution: 3.16 Å
Organism: Mus musculus
Chains: 4
Atoms: 9,973
Mol. weight: 151.92 kDa
Ligands: NAG
Released: 6 Jun 2018

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

Secondary structure: helices and β-sheets

5XWU contains 41 α-helices and 113 β-strands across 4 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: 9 helices, 30 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
α-helix	71	1
β-strand	76-80	5	1
β-strand	86-91	6	1
β-strand	102-108	7	3
β-strand	113-119	7	3
β-strand	120-123	4	2
α-helix	125-127	3
β-strand	134-137	4	4
β-strand	142-145	4	2
β-strand	150-152	3	5
β-strand	155-157	3	4
α-helix	161-162	2
β-strand	163-168	6	2
β-strand	171-172	2	2
β-strand	182-184	3	5
β-strand	199-201	3	5
α-helix	206-208	3
β-strand	210-217	8	2
β-strand	222-224	3	2
α-helix	225-227	3
β-strand	228-233	6	2
α-helix	234-235	2
β-strand	241-247	7	6
α-helix	248-251	4
β-strand	252-254	3	7
β-strand	259-269	11	6
α-helix	271-272	2
β-strand	273-278	6	7
β-strand	281-282	2	7
β-strand	291	1	7
β-strand	293-299	7	6
β-strand	305-313	9	7
β-strand	316-326	11	7

Chain B: 11 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	34-35	2
β-strand	39-41	3	8
β-strand	48-50	3	8
α-helix	59-60	2
β-strand	69-71	3	8
β-strand	79-80	2	9
β-strand	93-95	3	8
β-strand	103-104	2	9
β-strand	117-119	3	8
β-strand	127-128	2	10
β-strand	141-143	3	8
β-strand	151-152	2	10
α-helix	153	1
α-helix	158-160	3
β-strand	166-168	3	8
α-helix	179-182	4
β-strand	190-192	3	8
β-strand	214-216	3	8
β-strand	246-248	3	8
β-strand	254-255	2	11
α-helix	258-260	3
α-helix	261-264	4
β-strand	274	1	12
β-strand	275-277	3	11
α-helix	279-281	3
β-strand	285	1	12
α-helix	286-288	3
α-helix	291-293	3
β-strand	297-303	7	13
β-strand	317-319	3	14
β-strand	322-326	5	13
α-helix	328-329	2
β-strand	330-334	5	15
β-strand	340-341	2	15
β-strand	347-349	3	14
β-strand	355-357	3	14
β-strand	367-374	8	15
β-strand	377-384	8	15

Chain C: 10 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	29-35	7	16
β-strand	40-43	4	17
β-strand	48-57	10	16
α-helix	59-60	2
β-strand	61-66	6	18
β-strand	69-70	2	18
α-helix	71	1
β-strand	76-80	5	16
β-strand	86-91	6	16
β-strand	102-108	7	18
β-strand	113-119	7	18
β-strand	120-123	4	17
α-helix	125-127	3
α-helix	128-129	2
β-strand	134-137	4	19
β-strand	142-145	4	20
β-strand	150-152	3	21
β-strand	155-157	3	19
α-helix	161-162	2
β-strand	163-168	6	20
β-strand	171-172	2	20
β-strand	182-184	3	21
β-strand	199-201	3	21
α-helix	206-208	3
β-strand	210-217	8	20
β-strand	222-224	3	20
α-helix	225-227	3
β-strand	228-233	6	20
α-helix	234-235	2
β-strand	241-247	7	22
α-helix	248-251	4
β-strand	252-254	3	23
β-strand	259-269	11	22
α-helix	271-272	2
β-strand	273-278	6	23
β-strand	281-282	2	23
β-strand	291	1	23
β-strand	293-299	7	22
β-strand	305-313	9	23
β-strand	316-326	11	23

Chain D: 11 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	34-35	2
β-strand	39-41	3	24
β-strand	47-50	4	24
α-helix	59-60	2
β-strand	67-71	5	24
β-strand	79-80	2	25
β-strand	93-95	3	24
β-strand	103-104	2	25
β-strand	117-119	3	24
β-strand	127-128	2	26
β-strand	141-143	3	24
β-strand	151-152	2	26
α-helix	153	1
α-helix	158-160	3
β-strand	166-168	3	24
α-helix	179-182	4
β-strand	190-192	3	24
β-strand	214-216	3	24
β-strand	246-248	3	24
β-strand	254-255	2	27
α-helix	258-260	3
α-helix	261-264	4
β-strand	274	1	28
β-strand	275-277	3	27
α-helix	279-281	3
β-strand	285	1	28
α-helix	286-288	3
α-helix	291-293	3
β-strand	297-303	7	29
β-strand	319	1	30
β-strand	322-326	5	29
α-helix	328-329	2
β-strand	330-333	4	31
β-strand	349	1	30
β-strand	355	1	30
β-strand	367-374	8	31
β-strand	377-384	8	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor-type tyrosine-protein phosphatase delta	A, C	protein	313	Mus musculus	Q64487 (AlphaFold model)
Leucine-rich repeat and fibronectin type III domain-containing protein 1	B, D	protein	365	Mus musculus	Q2WF71 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5XWU_1 Receptor-type tyrosine-protein phosphatase delta (chains A, C)
LMGCVAETPPRFTRTPVDQTGVSGGVASFICQATGDPRPKIVWNKKGKKVSNQRFEVIEF
DDGSGSVLRIQPLRTPRDEAIYECVASNNVGEISVSTRLTVLREDQIPRGFPTIDMGPQL
KVVERTRTATMLCAASGNPDPEITWFKDFLPVDTSNNNGRIKQLRSESIGGTPIRGALQI
EQSEESDQGKYECVATNSAGTRYSAPANLYVRELREVRRVPPRFSIPPTNHEIMPGGSVN
ITCVAVGSPMPYVKWMLGAEDLTPEDDMPIGRNVLELNDVRQSANYTCVAMSTLGVIEAI
AQITVKAHHHHHH

Sequence of entity 2 (B, D), FASTA

>5XWU_2 Leucine-rich repeat and fibronectin type III domain-containing protein 1 (chains B, D)
QPCPGRCICQNVAPTLTMLCAKTGLLFVPPAIDRRVVELRLTDNFIAAVRRRDFANMTSL
VHLTLSRNTIGQVAAGAFADLRALRALHLDSNRLAEVRGDQLRGLGNLRHLILGNNQIRK
VESAAFDAFLSTVEDLDLSYNNLEALPWEAVGQMVNLNTLTLDHNLIDHIAEGTFVQLHK
LVRLDMTSNRLHKLPPDGLFLRSQGGGPKPPTPLTVSFGGNPLHCNCELLWLRRLTREDD
LETCATPEHLTDRYFWSIPEEEFLCEPPLITRQAGGRALVVEGQAVSLRCRAVGDPEPVV
HWVAPDGRLLGNSSRTRVRGDGTLDVTITTLRDSGTFTCIASNAAGEATAPVEVCVVPLH
HHHHH

Ligands and cofactors

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

Water and common crystallization additives (MES) are not listed.

Primary citation

Structural basis of trans-synaptic interactions between PTP delta and SALMs for inducing synapse formation. Goto-Ito, S., Yamagata, A., Sato, Y. et al. Nat Commun (2018) 9:269-269. DOI 10.1038/s41467-017-02417-z · 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
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
4YH7 4.4 Å, Crystal structure of PTPdelta ectodomain in complex with IL1RAPL1

Browse structure collections

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