9EOU: B1b2 domains from Human Neuropilin-1

Crystal Structure of the b1b2 domains from Human Neuropilin-1 in complex with a peptide. Determined by X-ray diffraction at 1.55 Å resolution. Released 26 Jun 2024.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,786
Mol. weight: 37.73 kDa
Released: 26 Jun 2024

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

Secondary structure: helices and β-sheets

9EOU contains 9 α-helices and 33 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: 9 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	27-28	2	1
α-helix	38-40	3
β-strand	41-43	3	1
α-helix	49-51	3
α-helix	53-56	4
β-strand	57	1	1
β-strand	65	1	2
β-strand	76-92	17	1
β-strand	94-95	2	3
β-strand	102-103	2	3
β-strand	104-113	10	1
β-strand	120-121	2	1
β-strand	123-124	2	4
β-strand	127-128	2	4
β-strand	131-132	2	1
β-strand	141-162	22	1
β-strand	167	1	2
β-strand	168-175	8	1
α-helix	176-178	3
β-strand	180	1	5
α-helix	181	1
α-helix	183-185	3
β-strand	187-190	4	5
α-helix	192-194	3
β-strand	196-199	4	5
α-helix	209-211	3
β-strand	213	1	5
β-strand	221-223	3	6
β-strand	235-251	17	5
β-strand	253-255	3	7
β-strand	258-260	3	7
β-strand	262-270	9	5
β-strand	277-278	2	5
α-helix	279	1
β-strand	280	1	8
β-strand	287	1	8
β-strand	290-291	2	5
β-strand	300-319	20	5
β-strand	320	1	9
β-strand	323	1	9
β-strand	324-326	3	6
β-strand	327-334	8	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuropilin-1	A	protein	318	Homo sapiens	O14786 (AlphaFold model)
Osteopontin	P	protein	15	Homo sapiens	P10451 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9EOU_1 Neuropilin-1 (chains A)
QGHMFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWIQV
DLGLLRFVTAVGTQGAISKETKKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTNPT
DVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKITDYPCSGMLGMVSGLISDSQIT
SSNQGDRNWMPENIRLVTSRSGWALPPAPHSYINEWLQIDLGEEKIVRGIIIQGGKHREN
KVFMRKFKIGYSNNGSDWKMIMDDSKRKAKSFEGNNNYDTPELRTFPALSTRFIRIYPER
ATHGGLGLRMELLGCEVE

Sequence of entity 2 (P), FASTA

>9EOU_2 Osteopontin (chains P)
VDTYDGGISVVYGLR

Primary citation

Identification of an osteopontin-derived peptide that binds neuropilin-1 and activates vascular repair responses and angiogenesis. Chen, Y., Gialeli, C., Shen, J. et al. Pharmacol Res (2024) 205:107259-107259. DOI 10.1016/j.phrs.2024.107259 · 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.
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

Browse structure collections

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