5XWT: PTPdelta Ig1-Fn1

Crystal structure of PTPdelta Ig1-Fn1 in complex with SALM5 LRR-Ig. Determined by X-ray diffraction at 4.18 Å resolution. Released 6 Jun 2018.

Method: X-ray diffraction
Resolution: 4.18 Å
Organisms: Mus musculus, Homo sapiens
Chains: 4
Atoms: 11,527
Mol. weight: 174.58 kDa
Ligands: NAG
Released: 6 Jun 2018

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

Secondary structure: helices and β-sheets

5XWT contains 26 α-helices and 129 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: 7 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	29-35	7	1
β-strand	41-43	3	2
β-strand	48-57	10	1
β-strand	61-66	6	3
β-strand	69-70	2	3
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	121-123	3	2
β-strand	134-137	4	4
α-helix	138-141	4
β-strand	142-145	4	5
β-strand	150-152	3	6
β-strand	155-157	3	4
α-helix	162	1
β-strand	163-168	6	5
β-strand	171-172	2	5
β-strand	182-184	3	6
β-strand	199-201	3	6
α-helix	206-208	3
β-strand	210-217	8	5
β-strand	222-224	3	5
β-strand	228-233	6	5
β-strand	244-247	4	7
β-strand	252-254	3	8
β-strand	259-267	9	7
α-helix	271-272	2
β-strand	273-277	5	8
β-strand	282	1	8
β-strand	291	1	8
β-strand	293-299	7	7
β-strand	305-313	9	8
β-strand	316-326	11	8
α-helix	329-336	8
β-strand	337-341	5	9
β-strand	345-349	5	9
β-strand	360-367	8	10
α-helix	373-374	2
β-strand	375-380	6	10
β-strand	384-388	5	9
β-strand	396-403	8	10
β-strand	408-411	4	10
α-helix	412-413	2
β-strand	415-416	2	10

Chain B: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	11
β-strand	32-36	5	11
β-strand	55-57	3	11
β-strand	65-66	2	12
β-strand	79-81	3	11
β-strand	89-90	2	12
β-strand	103-105	3	11
β-strand	113-114	2	13
β-strand	127-129	3	11
β-strand	137-138	2	13
β-strand	151-153	3	11
α-helix	164-167	4
β-strand	175-177	3	11
β-strand	199-201	3	11
α-helix	217-219	3
β-strand	234-236	3	11
β-strand	242-243	2	14
α-helix	246-248	3
α-helix	249-253	5
β-strand	262	1	15
β-strand	263-265	3	14
β-strand	273	1	15
α-helix	279-281	3
β-strand	288-292	5	16
β-strand	303-307	5	17
β-strand	308-311	4	16
β-strand	317-321	5	18
β-strand	326	1	18
α-helix	338-340	3
β-strand	341-346	6	17
β-strand	354-360	7	18
β-strand	367-371	5	18

Chain C: 7 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	29-35	7	19
β-strand	40-43	4	20
β-strand	48-57	10	19
β-strand	61-66	6	21
β-strand	69-70	2	21
β-strand	76-80	5	19
β-strand	86-91	6	19
β-strand	102-108	7	21
β-strand	113-119	7	21
β-strand	120-123	4	20
β-strand	134-137	4	22
α-helix	138-141	4
β-strand	142-145	4	23
β-strand	150-152	3	24
β-strand	155-157	3	22
α-helix	162	1
β-strand	163-168	6	23
β-strand	171-172	2	23
β-strand	182-184	3	24
α-helix	185-186	2
β-strand	199-201	3	24
α-helix	206-208	3
β-strand	210-217	8	23
β-strand	222-224	3	23
β-strand	228-233	6	23
β-strand	244-247	4	25
β-strand	252-254	3	26
β-strand	260-267	8	25
α-helix	271-272	2
β-strand	273-277	5	26
β-strand	282	1	26
β-strand	291	1	26
β-strand	293-298	6	25
β-strand	305-313	9	26
β-strand	316-326	11	26
α-helix	329-336	8
β-strand	337-341	5	27
β-strand	345-349	5	27
β-strand	360-366	7	28
β-strand	376-380	5	28
β-strand	384-388	5	27
β-strand	397-403	7	28
β-strand	408-411	4	28
α-helix	412-413	2
β-strand	415-416	2	28

Chain D: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	25-28	4	29
β-strand	33-36	4	29
β-strand	53-57	5	29
β-strand	65-66	2	30
β-strand	79-81	3	29
β-strand	89-90	2	30
β-strand	103-105	3	29
β-strand	113-114	2	31
β-strand	127-129	3	29
β-strand	137-138	2	31
β-strand	151-153	3	29
α-helix	164-167	4
β-strand	175-177	3	29
β-strand	199-201	3	29
α-helix	217-219	3
β-strand	234-236	3	29
β-strand	242-243	2	32
α-helix	246-248	3
α-helix	249-253	5
β-strand	262	1	33
β-strand	263-265	3	32
β-strand	273	1	33
α-helix	279-281	3
β-strand	288-292	5	34
β-strand	295-296	2	35
β-strand	305-307	3	36
β-strand	308-311	4	34
β-strand	317-321	5	35
β-strand	326	1	35
α-helix	338-340	3
β-strand	341-343	3	36
β-strand	353-360	8	35
β-strand	367-372	6	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor-type tyrosine-protein phosphatase delta	A, C	protein	402	Mus musculus	Q64487 (AlphaFold model)
Leucine-rich repeat and fibronectin type-III domain-containing protein 5	B, D	protein	367	Homo sapiens	Q96NI6 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5XWT_1 Receptor-type tyrosine-protein phosphatase delta (chains A, C)
LMGCVAETPPRFTRTPVDQTGVSGGVASFICQATGDPRPKIVWNKKGKKVSNQRFEVIEF
DDGSGSVLRIQPLRTPRDEAIYECVASNNVGEISVSTRLTVLREDQIPRGFPTIDMGPQL
KVVERTRTATMLCAASGNPDPEITWFKDFLPVDTSNNNGRIKQLRSESIGGTPIRGALQI
EQSEESDQGKYECVATNSAGTRYSAPANLYVRELREVRRVPPRFSIPPTNHEIMPGGSVN
ITCVAVGSPMPYVKWMLGAEDLTPEDDMPIGRNVLELNDVRQSANYTCVAMSTLGVIEAI
AQITVKALPKPPGTPVVTESTATSITLTWDSGNPEPVSYYIIQHKPKNSEEPYKEIDGIA
TTRYSVAGLSPYSDYEFRVVAVNNIGRGPASEPVLTHHHHHH

Sequence of entity 2 (B, D), FASTA

>5XWT_2 Leucine-rich repeat and fibronectin type-III domain-containing protein 5 (chains B, D)
QICPKRCVCQILSPNLATLCAKKGLLFVPPNIDRRTVELRLADNFVTNIKRKDFANMTSL
VDLTLSRNTISFITPHAFADLRNLRALHLNSNRLTKITNDMFSGLSNLHHLILNNNQLTL
ISSTAFDDVFALEELDLSYNNLETIPWDAVEKMVSLHTLSLDHNMIDNIPKGTFSHLHKM
TRLDVTSNKLQKLPPDPLFQRAQVLATSGIISPSTFALSFGGNPLHCNCELLWLRRLSRE
DDLETCASPPLLTGRYFWSIPEEEFLCEPPLITRHTHEMRVLEGQRATLRCKARGDPEPA
IHWISPEGKLISNATRSLVYDNGTLDILITTVKDTGAFTCIASNPAGEATQIVDLHIIKL
PHHHHHH

Ligands and cofactors

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

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
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
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
4YH7 4.4 Å, Crystal structure of PTPdelta ectodomain in complex with IL1RAPL1

Browse structure collections

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