3NFL: PTPN4 PDZ domain

Crystal structure of the PTPN4 PDZ domain complexed with the C-terminus of the GluN2A NMDA receptor subunit. Determined by X-ray diffraction at 1.91 Å resolution. Released 24 Aug 2011.

Method: X-ray diffraction
Resolution: 1.91 Å
Organism: Homo sapiens
Chains: 8
Atoms: 3,115
Mol. weight: 54.43 kDa
Released: 24 Aug 2011

Explore 3NFL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3NFL contains 20 α-helices and 30 β-strands across 8 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, 8 β-strands

Element	Residues	Length	Sheet
β-strand	516-520	5	1
β-strand	530-535	6	1
α-helix	536-538	3
β-strand	540-547	8	1
α-helix	552-555	4
α-helix	559-560	2
α-helix	564	1
β-strand	565-569	5	1
β-strand	572-573	2	1
α-helix	579-587	9
α-helix	589-591	3
β-strand	593	1	2
β-strand	596	1	2
β-strand	597-602	6	1

Chain B: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	516-520	5	3
β-strand	530-535	6	3
β-strand	540-547	8	3
α-helix	552-555	4
α-helix	559-560	2
α-helix	564	1
β-strand	565-569	5	3
β-strand	572-573	2	3
α-helix	579-587	9
β-strand	597-602	6	3

Chain C: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	516-520	5	4
β-strand	530-535	6	4
α-helix	536-538	3
β-strand	540-547	8	4
α-helix	552-555	4
α-helix	559-560	2
α-helix	564	1
β-strand	565-569	5	4
β-strand	572-573	2	4
α-helix	579-587	9
β-strand	597-602	6	4

Chain D: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	516-520	5	5
β-strand	530-535	6	5
α-helix	536-538	3
β-strand	540-547	8	5
α-helix	552-555	4
α-helix	559-560	2
α-helix	564	1
β-strand	565-569	5	5
β-strand	572-573	2	5
α-helix	579-586	8
β-strand	597-602	6	5

Chains E, F, G and H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	13-15	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tyrosine-protein phosphatase non-receptor type 4	A, B, C, D	protein	107	Homo sapiens	P29074 (AlphaFold model)
Glutamate [NMDA] receptor subunit epsilon-1	E, F, G, H	protein	16	Homo sapiens	Q12879 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>3NFL_1 Tyrosine-protein phosphatase non-receptor type 4 (chains A, B, C, D)
GSSPEKPTPNGGIPHDNLVLIRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCV
PRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCERHSGELMLLVRPN

Sequence of entity 2 (E, F, G, H), FASTA

>3NFL_2 Glutamate [NMDA] receptor subunit epsilon-1 (chains E, F, G, H)
SNRRVYKKMPSIESDV

Primary citation

Peptides Targeting the PDZ Domain of PTPN4 Are Efficient Inducers of Glioblastoma Cell Death. Babault, N., Cordier, F., Lafage, M. et al. Structure (2011) 19:1518-1524. DOI 10.1016/j.str.2011.07.007 · PubMed

Other PDB entries of the same protein (UniProt P29074 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3NFK 1.43 Å, Crystal structure of the PTPN4 PDZ domain complexed with the C-terminus of a rabies…
2VPH 1.9 Å, Crystal structure of the human protein tyrosine phosphatase, non- receptor type 4, PDZ…
5EYZ 2.09 Å, Crystal structure of the PTPN4 PDZ domain complexed with the tailored peptide CYTO8-retev
5EZ0 2.35 Å, Crystal structure of the PTPN4 PDZ domain complexed with the PDZ binding motif of the…
2I75 2.45 Å, Crystal Structure of Human Protein Tyrosine Phosphatase N4 (PTPN4)
7VZE 2.88 Å, Crystal structure of PTPN4 PDZ bound to the PBM of HPV16 E6
2CS5 Solution structure of PDZ domain of Protein tyrosine phosphatase, non-receptor type 4

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