5C7G: B1 Domain of Human Neuropilin-1

Crystal Structure of the b1 Domain of Human Neuropilin-1 in complex with a bicine molecule. Determined by X-ray diffraction at 1.45 Å resolution. Released 6 Jul 2016.

Method: X-ray diffraction
Resolution: 1.45 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,528
Mol. weight: 18.61 kDa
Ligands: BCN
Released: 6 Jul 2016

Explore 5C7G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5C7G contains 4 α-helices and 15 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: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	1
α-helix	16-18	3
β-strand	19-21	3	1
α-helix	27-29	3
α-helix	31-34	4
β-strand	35	1	1
β-strand	43	1	2
β-strand	54-70	17	1
β-strand	72-73	2	3
β-strand	80-81	2	3
β-strand	82-91	10	1
β-strand	98-99	2	1
β-strand	101	1	4
β-strand	106	1	4
α-helix	107	1
β-strand	109-110	2	1
β-strand	119-140	22	1
β-strand	145	1	2
β-strand	146-152	7	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuropilin-1	A	protein	161	Homo sapiens	O14786 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5C7G_1 Neuropilin-1 (chains A)
HHHHHHFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWTPGEDSYREWI
QVDLGLLRFVTAVGTQGAISKETKKKYYVKTYKIDVSSNGEDWITIKEGNKPVLFQGNTN
PTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKIT

Ligands and cofactors

ID	Name	Formula	Copies
BCN	Bicine	C6 H13 N O4	1

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

Primary citation

Design, synthesis and biological evaluation of new peptidomimetic compounds targeting NRP-1 receptor TO BE PUBLISHED. Richard, M., Pelligrini Moise, N., Jelsch, C. 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
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.
7P5U 1.6 Å, Neuropilin-b1 in a complex with a VEGFB-derived peptide

Browse structure collections

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