5XNP: Human SALM5

Crystal structures of human SALM5 in complex with human PTPdelta. Determined by X-ray diffraction at 3.73 Å resolution. Released 24 Jan 2018.

Method: X-ray diffraction
Resolution: 3.73 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,418
Mol. weight: 148.14 kDa
Ligands: NAG, CA
Released: 24 Jan 2018

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

Secondary structure: helices and β-sheets

5XNP contains 30 α-helices and 108 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, 26 β-strands

Element	Residues	Length	Sheet
β-strand	25-27	3	1
β-strand	33-36	4	1
β-strand	53-57	5	1
β-strand	65-66	2	2
α-helix	68-71	4
β-strand	79-81	3	1
β-strand	89-90	2	2
β-strand	103-105	3	1
β-strand	113-114	2	3
β-strand	127-129	3	1
β-strand	137-138	2	3
β-strand	151-153	3	1
α-helix	164-167	4
β-strand	175-177	3	1
β-strand	199-201	3	1
α-helix	214-217	4
β-strand	234-236	3	1
β-strand	241-243	3	4
α-helix	246-248	3
α-helix	249-252	4
β-strand	262-265	4	4
α-helix	267-269	3
β-strand	273	1	4
α-helix	279-281	3
β-strand	285-292	8	5
β-strand	295-297	3	6
β-strand	304-306	3	7
β-strand	308-313	6	5
α-helix	315-316	2
β-strand	317-321	5	6
β-strand	335-336	2	7
β-strand	342-344	3	7
α-helix	349-351	3
β-strand	353-360	8	6
β-strand	365-373	9	6

Chain B: 9 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	25-27	3	8
β-strand	33-36	4	8
β-strand	53-57	5	8
β-strand	65-66	2	9
β-strand	79-81	3	8
β-strand	89-90	2	9
β-strand	103-105	3	8
β-strand	113-114	2	10
β-strand	127-129	3	8
β-strand	137-138	2	10
β-strand	151-153	3	8
α-helix	164-167	4
β-strand	175-177	3	8
β-strand	199-201	3	8
α-helix	214-217	4
β-strand	234-236	3	8
β-strand	241-243	3	11
α-helix	246-248	3
α-helix	249-252	4
β-strand	262-265	4	11
α-helix	267-269	3
β-strand	273	1	11
α-helix	274-276	3
α-helix	279-281	3
β-strand	285-292	8	12
β-strand	295-297	3	13
β-strand	306	1	14
β-strand	308-313	6	12
α-helix	315-316	2
β-strand	317-321	5	13
β-strand	335-336	2	14
β-strand	342-343	2	14
α-helix	349-351	3
β-strand	353-360	8	13
β-strand	365-373	9	13

Chains D and E: 6 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	15
β-strand	33-35	3	16
β-strand	41-50	10	15
α-helix	52-53	2
β-strand	54-59	6	16
β-strand	62-63	2	16
β-strand	69-73	5	15
β-strand	79-84	6	15
β-strand	94-101	8	16
β-strand	106-115	10	16
α-helix	121-122	2
β-strand	127-130	4	17
β-strand	135-138	4	18
β-strand	143-145	3	19
β-strand	148-150	3	17
α-helix	154-155	2
β-strand	156-161	6	18
β-strand	164-165	2	18
β-strand	175-177	3	19
β-strand	183-185	3	19
β-strand	194-202	9	18
β-strand	205-208	4	18
α-helix	209-211	3
β-strand	212-217	6	18
β-strand	225-231	7	20
α-helix	232-235	4
β-strand	236	1	21
β-strand	245-253	9	20
α-helix	255-256	2
β-strand	257-262	6	21
β-strand	265-266	2	21
β-strand	277-281	5	20
β-strand	289-297	9	21
β-strand	300-308	9	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leucine-rich repeat and fibronectin type-III domain-containing protein 5	A, B	protein	361	Homo sapiens	Q96NI6 (AlphaFold model)
Receptor-type tyrosine-protein phosphatase delta	D, E	protein	291	Homo sapiens	P23468 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5XNP_1 Leucine-rich repeat and fibronectin type-III domain-containing protein 5 (chains A, B)
PGDPQICPKRCVCQILSPNLATLCAKKGLLFVPPNIDRRTVELRLADNFVTNIKRKDFAN
MTSLVDLTLSRNTISFITPHAFADLRNLRALHLNSNRLTKITNDMFSGLSNLHHLILNNN
QLTLISSTAFDDVFALEELDLSYNNLETIPWDAVEKMVSLHTLSLDHNMIDNIPKGTFSH
LHKMTRLDVTSNKLQKLPPDPLFQRAQVLATSGIISPSTFALSFGGNPLHCNCELLWLRR
LSREDDLETCASPPLLTGRYFWSIPEEEFLCEPPLITRHTHEMRVLEGQRATLRCKARGD
PEPAIHWISPEGKLISNATRSLVYDNGTLDILITTVKDTGAFTCIASNPAGEATQIVDLH
I

Sequence of entity 2 (D, E), FASTA

>5XNP_2 Receptor-type tyrosine-protein phosphatase delta (chains D, E)
ETPPRFTRTPVDQTGVSGGVASFICQATGDPRPKIVWNKKGKKVSNQRFEVIEFDDGSGS
VLRIQPLRTPRDEAIYECVASNNVGEISVSTRLTVLREDQIPRGFPTIDMGPQLKVVERT
RTATMLCAASGNPDPEITWFKDFLPVDTSNNNGRIKQLRSGALQIEQSEESDQGKYECVA
TNSAGTRYSAPANLYVRELREVRRVPPRFSIPPTNHEIMPGGSVNITCVAVGSPMPYVKW
MLGAEDLTPEDDMPIGRNVLELNDVRQSANYTCVAMSTLGVIEAIAQITVK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8
CA	Calcium ion	Ca	12

Water and common crystallization additives (NA, CL, SO4) are not listed.

Primary citation

Structural basis of SALM5-induced PTP delta dimerization for synaptic differentiation. Lin, Z., Liu, J., Ding, H. et al. Nat Commun (2018) 9:268-268. DOI 10.1038/s41467-017-02414-2 · PubMed

Other PDB entries of the same protein (UniProt Q96NI6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5XNQ 2.8 Å, Crystal structures of human SALM5
5XWS 3.08 Å, Crystal structure of SALM5 LRR-Ig
5XWT 4.18 Å, Crystal structure of PTPdelta Ig1-Fn1 in complex with SALM5 LRR-Ig

Browse structure collections

About this viewer

MolViewer shows 5XNP 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.