2QQM: A2b1b2 Domains from Human Neuropilin-1

Crystal Structure of the a2b1b2 Domains from Human Neuropilin-1. Determined by X-ray diffraction at 2.0 Å resolution. Released 20 Nov 2007.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,754
Mol. weight: 52.3 kDa
Ligands: CA
Released: 20 Nov 2007

Explore 2QQM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2QQM contains 11 α-helices and 39 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: 11 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	149-151	3	1
β-strand	155-159	5	2
α-helix	166-168	3
β-strand	172-178	7	1
α-helix	180-182	3
β-strand	185-193	9	2
β-strand	210-214	5	1
α-helix	222	1
β-strand	223-227	5	1
β-strand	235-238	4	2
β-strand	242-248	7	1
β-strand	257-264	8	2
α-helix	265-268	4
β-strand	277-278	2	3
α-helix	288-290	3
β-strand	291-293	3	3
α-helix	299-301	3
α-helix	303-306	4
β-strand	307	1	3
β-strand	315	1	4
β-strand	326-342	17	3
β-strand	344-345	2	5
β-strand	352-353	2	5
β-strand	354-363	10	3
β-strand	369-371	3	3
β-strand	373	1	6
β-strand	378	1	6
β-strand	381-382	2	3
β-strand	391-412	22	3
β-strand	417	1	4
β-strand	418-424	7	3
α-helix	426-428	3
β-strand	433-434	2	7
α-helix	444-446	3
β-strand	447-449	3	7
α-helix	459-462	4
β-strand	463	1	7
β-strand	471-473	3	8
β-strand	485-501	17	7
β-strand	512-520	9	7
β-strand	527-528	2	7
α-helix	529	1
β-strand	530	1	9
β-strand	537	1	9
β-strand	540-541	2	7
β-strand	550-569	20	7
β-strand	570	1	10
β-strand	573	1	10
β-strand	574-576	3	8
β-strand	577-583	7	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuropilin-1	A	protein	450	Homo sapiens	O14786 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2QQM_1 Neuropilin-1 (chains A)
GSHMFKRGPECSQNYTTPSGVIKSPGFPEKYPNSLECTYIVFAPKMSEIILEFESFDLEP
DSNPPGGMFCRYDRLEIWDGFPDVGPHIGRYCGQKTPGRIRSSSGILSMVFYTDSAIAKE
GFSANYSVLQSSVSEDFKCMEALGMESGEIHSDQITASSQYSTNWSAERSRLNYPENGWT
PGEDSYREWIQVDLGLLRFVTAVGTQGAISKETKKKYYVKTYKIDVSSNGEDWITIKEGN
KPVLFQGNTNPTDVVVAVFPKPLITRFVRIKPATWETGISMRFEVYGCKITDYPCSGMLG
MVSGLISDSQITSSNQGDRNWMPENIRLVTSRSGWALPPAPHSYINEWLQIDLGEEKIVR
GIIIQGGKHRENKVFMRKFKIGYSNNGSDWKMIMDDSKRKAKSFEGNNNYDTPELRTFPA
LSTRFIRIYPERATHGGLGLRMELLGCEVE

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

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

Primary citation

Structural studies of neuropilin/antibody complexes provide insights into semaphorin and VEGF binding. Appleton, B.A., Wu, P., Maloney, J. et al. EMBO J (2007) 26:4902-4912. DOI 10.1038/sj.emboj.7601906 · 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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