7P5U: Neuropilin-1

Neuropilin-b1 in a complex with a VEGFB-derived peptide. Determined by X-ray diffraction at 1.6 Å resolution. Released 27 Jul 2022.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,772
Mol. weight: 38.92 kDa
Released: 27 Jul 2022

Explore 7P5U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7P5U contains 6 α-helices and 32 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 AAA: 3 helices, 16 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	321	1	3
β-strand	326-342	17	1
β-strand	344-345	2	4
β-strand	352-353	2	4
β-strand	354-363	10	1
β-strand	370-371	2	1
β-strand	373-374	2	5
β-strand	377-378	2	5
β-strand	381-382	2	1
β-strand	391-412	22	1
β-strand	417	1	2
β-strand	418-424	7	1

Chain BBB: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	277-278	2	6
α-helix	288-290	3
β-strand	291-293	3	6
β-strand	298	1	3
α-helix	299-301	3
α-helix	303-306	4
β-strand	307	1	6
β-strand	315	1	7
β-strand	326-342	17	6
β-strand	344-345	2	8
β-strand	352-353	2	8
β-strand	354-363	10	6
β-strand	369-371	3	6
β-strand	373-374	2	9
β-strand	377-378	2	9
β-strand	381-382	2	6
β-strand	391-412	22	6
β-strand	417	1	7
β-strand	418-425	8	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuropilin-1	AAA, BBB	protein	158	Homo sapiens	O14786 (AlphaFold model)
MGC0122	CCC, EEE	protein	13	Homo sapiens

Sequence of entity 1 (AAA, BBB), FASTA

>7P5U_1 Neuropilin-1 (chains AAA, BBB)
GHMFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVD
LGLLRFVTAVGTQGAISKETKKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTD
VVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT

Sequence of entity 2 (CCC, EEE), FASTA

>7P5U_2 MGC0122 (chains CCC, EEE)
DRAATPHHRPQPR

Primary citation

Peptides Derived from Vascular Endothelial Growth Factor B Show Potent Binding to Neuropilin-1. Mota, F., Yelland, T., Hutton, J.A. et al. Chembiochem (2022) 23:e202100463-e202100463. DOI 10.1002/cbic.202100463 · 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
8PFE 1.35 Å, Crystal Structure of an Hexavariant of the b1 Domain of Human Neuropilin-1 in Complex…
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.

Browse structure collections

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