4RCA: Human PTPdelta and human Slitrk1 complex

Crystal structure of human PTPdelta and human Slitrk1 complex. Determined by X-ray diffraction at 2.99 Å resolution. Released 19 Nov 2014.

Method: X-ray diffraction
Resolution: 2.99 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,287
Mol. weight: 63.28 kDa
Ligands: NAG
Released: 19 Nov 2014

Explore 4RCA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4RCA contains 16 α-helices and 48 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: 9 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	25-28	4	1
β-strand	33-36	4	2
β-strand	41-48	8	1
α-helix	52-53	2
β-strand	54-59	6	2
β-strand	62-63	2	2
α-helix	64	1
β-strand	69-73	5	1
β-strand	79-84	6	1
β-strand	94-101	8	2
β-strand	106-116	11	2
α-helix	121-122	2
β-strand	127-130	4	3
β-strand	135-138	4	4
β-strand	143-145	3	5
β-strand	148-150	3	3
α-helix	154-155	2
β-strand	156-161	6	4
β-strand	164-165	2	4
β-strand	175-177	3	5
α-helix	187	1
β-strand	188	1	3
β-strand	192-194	3	5
β-strand	203-210	8	4
β-strand	215-217	3	4
α-helix	218-220	3
β-strand	221-226	6	4
β-strand	234-240	7	6
α-helix	241-244	4
β-strand	245-247	3	7
β-strand	251-262	12	6
α-helix	264-265	2
β-strand	266-271	6	7
β-strand	274-275	2	7
α-helix	279-281	3
β-strand	284	1	7
β-strand	286-294	9	6
β-strand	298-306	9	7
β-strand	309-319	11	7

Chain B: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	8
β-strand	38-41	4	8
β-strand	61-64	4	8
β-strand	72-73	2	9
α-helix	79-81	3
β-strand	84-88	5	8
β-strand	96-97	2	9
β-strand	110-112	3	8
β-strand	120-121	2	10
β-strand	134-136	3	8
β-strand	144-145	2	10
α-helix	147-149	3
β-strand	158-160	3	8
β-strand	181-183	3	8
α-helix	194-198	5
β-strand	206-208	3	8
β-strand	214-215	2	11
α-helix	221-229	9
α-helix	231	1
β-strand	235	1	8
β-strand	240	1	12
β-strand	241-243	3	11
β-strand	251	1	12
α-helix	252-254	3
α-helix	257-260	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Receptor-type tyrosine-protein phosphatase delta	A	protein	308	Homo sapiens	P23468 (AlphaFold model)
SLIT and NTRK-like protein 1	B	protein	251	Homo sapiens	Q96PX8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4RCA_1 Receptor-type tyrosine-protein phosphatase delta (chains A)
ETPPRFTRTPVDQTGVSGGVASFICQATGDPRPKIVWNKKGKKVSNQRFEVIEFDDGSGS
VLRIQPLRTPRDEAIYECVASNNVGEISVSTRLTVLREDQIPRGFPTIDMGPQLKVVERT
RTATMLCAASGNPDPEITWFKDFLPVDTSNNNGRIKQLRSESIGGTPIRGALQIEQSEES
DQGKYECVATNSAGTRYSAPANLYVRELREVRRVPPRFSIPPTNHEIMPGGSVNITCVAV
GSPMPYVKWMLGAEDLTPEDDMPIGRNVLELNDVRQSANYTCVAMSTLGVIEAIAQITVK
ALSRLVPR

Sequence of entity 2 (B), FASTA

>4RCA_2 SLIT and NTRK-like protein 1 (chains B)
TGDVCKEKICSCNEIEGDLHVDCEKKGFTSLQRFTAPTSQFYHLFLHGNSLTRLFPNEFA
NFYNAVSLHMENNGLHEIVPGAFLGLQLVKRLHINNNKIKSFRKQTFLGLDDLEYLQADF
NLLRDIDPGAFQDLNKLEVLILNDNLISTLPANVFQYVPITHLDLRGNRLKTLPYEEVLE
QIPGIAEILLEDNPWDCTCDLLSLKEWLENIPKNALIGRVVCEAPTRLQGKDLNETTEQD
LCPLKSRLVPR

Ligands and cofactors

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

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

Primary citation

Structural basis for LAR-RPTP/Slitrk complex-mediated synaptic adhesion. Um, J.W., Kim, K.H., Park, B.S. et al. Nat Commun (2014) 5:5423-5423. DOI 10.1038/ncomms6423 · 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…
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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