9S57: Neuropilin-1

The b1 and b2 domains of neuropilin-1 with a bound VGF TLQP-21 peptide. Determined by X-ray diffraction at 1.57 Å resolution. Released 12 Aug 2026.

Method: X-ray diffraction
Resolution: 1.57 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,916
Mol. weight: 38.38 kDa
Released: 12 Aug 2026

Explore 9S57 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9S57 contains 8 α-helices and 32 β-strands across 1 chain. 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: 8 helices, 32 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
α-helix	426-428	3
β-strand	430	1	5
α-helix	431	1
α-helix	433-435	3
β-strand	437-440	4	5
α-helix	442-444	3
β-strand	446-449	4	5
α-helix	459-461	3
β-strand	471-473	3	6
β-strand	485-501	17	5
β-strand	503-505	3	7
β-strand	508-510	3	7
β-strand	512-520	9	5
β-strand	527-528	2	5
β-strand	530	1	8
β-strand	537	1	8
β-strand	540-541	2	5
β-strand	550-569	20	5
β-strand	570	1	9
β-strand	573	1	9
β-strand	574-576	3	6
β-strand	577-584	8	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuropilin-1	A	protein	316	Homo sapiens	O14786 (AlphaFold model)
Neurosecretory protein VGF	B	protein	21	Homo sapiens	O15240 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9S57_1 Neuropilin-1 (chains A)
SMFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDL
GLLRFVTAVGTQGAISKETKKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDV
VVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKITDYPCSGMLGMVSGLISDSQITSS
NQGDRNWMPENIRLVTSRSGWALPPAPHSYINEWLQIDLGEEKIVRGIIIQGGKHRENKV
FMRKFKIGYSNNGSDWKMIMDDSKRKAKSFEGNNNYDTPELRTFPALSTRFIRIYPERAT
HGGLGLRMELLGCEVE

Sequence of entity 2 (B), FASTA

>9S57_2 Neurosecretory protein VGF (chains B)
TLQPPSALRRRHYHHALPPSR

Primary citation

The b1 and b2 domains of neuropilin-1 with a bound VGF TLQP-21 peptide. Bradshaw, W.J., Wilkes, A.J.R., Randall, G.T. et al. To be published.

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
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

Browse structure collections

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