8PFE: Neuropilin-1

Crystal Structure of an Hexavariant of the b1 Domain of Human Neuropilin-1 in Complex with the KDKPPR Peptide. Determined by X-ray diffraction at 1.35 Å resolution. Released 2 Aug 2023.

Method: X-ray diffraction
Resolution: 1.35 Å
Organisms: Homo sapiens, unidentified
Chains: 4
Atoms: 2,977
Mol. weight: 42.13 kDa
Released: 2 Aug 2023

Explore 8PFE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PFE contains 6 α-helices and 30 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: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	277-278	2	1
α-helix	288-290	3
β-strand	291-293	3	1
α-helix	299-301	3
α-helix	303-306	4
β-strand	307	1	1
β-strand	315	1	2
β-strand	326-342	17	1
β-strand	344-345	2	3
β-strand	352-353	2	3
β-strand	354-363	10	1
β-strand	370-371	2	1
β-strand	373-374	2	4
β-strand	377-378	2	4
β-strand	381-382	2	1
β-strand	391-412	22	1
β-strand	417	1	2
β-strand	418-424	7	1

Chain C: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	277-278	2	5
α-helix	288-290	3
β-strand	291-293	3	5
α-helix	299-301	3
α-helix	303-306	4
β-strand	307	1	5
β-strand	315	1	6
β-strand	326-342	17	5
β-strand	344-345	2	7
β-strand	352-353	2	7
β-strand	354-363	10	5
β-strand	370-371	2	5
β-strand	373	1	8
β-strand	378	1	8
β-strand	381-382	2	5
β-strand	391-412	22	5
β-strand	417	1	6
β-strand	418-424	7	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuropilin-1	A, C	protein	180	Homo sapiens	O14786 (AlphaFold model)
Lys-asp-lys-pro-pro-arg	B, D	protein	6	unidentified

Sequence of entity 1 (A, C), FASTA

>8PFE_1 Neuropilin-1 (chains A, C)
MGSSHHHHHHGSGSGLEVLFQGPHMFKCMKALGMESGKIHSKQITASSQYSTNWSAERSR
LNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKETKKKYYVKTYKIDVSSNGK
DWITIEEGNKPVLFQGNTNPTDVVVAVFPEPLITRFVRIKPATWETGISMRFEVYGCKIT

Sequence of entity 2 (B, D), FASTA

>8PFE_2 LYS-ASP-LYS-PRO-PRO-ARG (chains B, D)
KDKPPR

Primary citation

New Crystal Form of Human Neuropilin-1 b1 Fragment with Six Electrostatic Mutations Complexed with KDKPPR Peptide Ligand. Goudiaby, I., Malliavin, T.E., Mocchetti, E. et al. Molecules (2023) 28. DOI 10.3390/molecules28145603 · PubMed

Other PDB entries of the same protein (UniProt O14786 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6FMC 0.9 Å, Neuropilin1-b1 domain in complex with EG01377, 0.9 Angstrom structure
6TKK 1.06 Å, Neuropilin 1-b1 domain in a complex with the C-terminal VEGFB186 peptide
5JGI 1.38 Å, X-ray structure of neuropilin-1 b1 domain complexed with M45 compound
5C7G 1.45 Å, Crystal Structure of the b1 Domain of Human Neuropilin-1 in complex with a bicine molecule
5IJR 1.52 Å, X-ray structure of neuropilin-1 b1 domain complexed with Arg-1 ligand.
9EOU 1.55 Å, Crystal Structure of the b1b2 domains from Human Neuropilin-1 in complex with a peptide.
7O1N 1.56 Å, Crystal Structure of Human Neuropilin-1 b1 Domain mutant - Y297A
9S57 1.57 Å, The b1 and b2 domains of neuropilin-1 with a bound VGF TLQP-21 peptide
9F6B 1.57 Å, Human neuropilin-1 in a complex with a quinoline based antagonists
5IYY 1.6 Å, X-ray structure of neuropilin-1 b1 domain complexed with Arg-4 ligand.
5JGQ 1.6 Å, X-ray structure of neuropilin-1 b1 domain complexed with Arg-7 ligand.
7P5U 1.6 Å, Neuropilin-b1 in a complex with a VEGFB-derived peptide

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