5J1X: Neuropilin-1 b1 domain

X-ray structure of neuropilin-1 b1 domain complexed with Arg-5 ligand. Determined by X-ray diffraction at 2.1 Å resolution. Released 5 Apr 2017.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,503
Mol. weight: 72.84 kDa
Ligands: AR5
Released: 5 Apr 2017

Explore 5J1X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5J1X contains 14 α-helices and 60 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.

Chains A and B: 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

Chains C and D: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	277-278	2	9
α-helix	288-290	3
β-strand	291-293	3	9
α-helix	299-301	3
α-helix	303-306	4
β-strand	307	1	9
β-strand	315	1	10
β-strand	326-342	17	9
β-strand	344-345	2	11
β-strand	352-353	2	11
β-strand	354-363	10	9
β-strand	370-371	2	9
β-strand	373-374	2	12
β-strand	377-378	2	12
α-helix	379	1
β-strand	381-382	2	9
β-strand	391-412	22	9
β-strand	417	1	10
β-strand	418-424	7	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuropilin-1	A, B, C, D	protein	158	Homo sapiens	O14786 (AlphaFold model)

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

>5J1X_1 Neuropilin-1 (chains A, B, C, D)
GHMFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVD
LGLLRFVTAVGTQGAISKETKKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTD
VVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT

Ligands and cofactors

ID	Name	Formula	Copies
AR5	N~2~-(tert-butoxycarbonyl)-L-arginine	C11 H22 N4 O4	4

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

Primary citation

Architecture and hydration of the arginine-binding site of neuropilin-1. Mota, F., Fotinou, C., Rana, R.R. et al. FEBS J (2018) 285:1290-1304. DOI 10.1111/febs.14405 · 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.

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