9S56: Neuropilin-1

The b1 and b2 domains of neuropilin-1 with a bound VGF TLQP-21 peptide. Determined by X-ray diffraction at 1.67 Å resolution. Released 12 Aug 2026.

Method: X-ray diffraction
Resolution: 1.67 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,883
Mol. weight: 39.64 kDa
Ligands: TCH, CPS
Released: 12 Aug 2026

Explore 9S56 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9S56 contains 5 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: 5 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
β-strand	430-431	2	5
β-strand	434-435	2	5
β-strand	438-440	3	6
α-helix	442-444	3
β-strand	446-449	4	6
α-helix	459-462	4
β-strand	463	1	6
β-strand	471-473	3	7
β-strand	485-501	17	6
β-strand	503-505	3	8
β-strand	508-510	3	8
β-strand	515-520	6	6
β-strand	527-528	2	6
β-strand	530	1	9
β-strand	537	1	9
β-strand	540	1	6
β-strand	550-566	17	6
β-strand	574-576	3	7
β-strand	577-583	7	6

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

>9S56_1 Neuropilin-1 (chains A)
SMFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQVDL
GLLRFVTAVGTQGAISKETKKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPTDV
VVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKITDYPCSGMLGMVSGLISDSQITSS
NQGDRNWMPENIRLVTSRSGWALPPAPHSYINEWLQIDLGEEKIVRGIIIQGGKHRENKV
FMRKFKIGYSNNGSDWKMIMDDSKRKAKSFEGNNNYDTPELRTFPALSTRFIRIYPERAT
HGGLGLRMELLGCEVE

Sequence of entity 2 (B), FASTA

>9S56_2 Neurosecretory protein VGF (chains B)
TLQPPSALRRRHYHHALPPSR

Ligands and cofactors

ID	Name	Formula	Copies
TCH	Taurocholic acid	C26 H45 N O7 S	1
CPS	3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate	C32 H58 N2 O7 S	1

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

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
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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