2QQJ: B1b2 Domains from Human Neuropilin-2

Crystal Structure of the b1b2 Domains from Human Neuropilin-2. Determined by X-ray diffraction at 1.95 Å resolution. Released 20 Nov 2007.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,754
Mol. weight: 36.78 kDa
Released: 20 Nov 2007

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

Secondary structure: helices and β-sheets

2QQJ contains 6 α-helices and 30 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: 6 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	279-280	2	1
α-helix	290-292	3
β-strand	293-295	3	1
α-helix	306-308	3
β-strand	310	1	1
β-strand	318	1	2
β-strand	329-345	17	1
β-strand	347-348	2	3
β-strand	355-356	2	3
β-strand	357-366	10	1
β-strand	373-374	2	1
β-strand	376-377	2	4
β-strand	380-381	2	4
β-strand	384-385	2	1
β-strand	394-415	22	1
β-strand	420	1	2
β-strand	421-427	7	1
α-helix	429-431	3
β-strand	436-437	2	5
α-helix	447-449	3
β-strand	450-452	3	5
α-helix	462-465	4
β-strand	466	1	5
β-strand	474	1	6
β-strand	488-504	17	5
β-strand	506	1	7
β-strand	519	1	7
β-strand	521-529	9	5
β-strand	536-537	2	5
α-helix	538	1
β-strand	539-540	2	8
β-strand	545-546	2	8
β-strand	549-550	2	5
β-strand	559-578	20	5
β-strand	585	1	6
β-strand	586-593	8	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuropilin-2	A	protein	325	Homo sapiens	O60462 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2QQJ_1 Neuropilin-2 (chains A)
GSHMFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQ
VDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDA
TEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTDAPCSNMLGMLSGLIADSQI
SASSTQEYLWSPSAARLVSSRSGWFPRIPQAQPGEEWLQVDLGTPKTVKGVIIQGARGGD
SITAVEARAFVRKFKVSYSLNGKDWEYIQDPRTQQPKLFEGNMHYDTPDIRRFDPIPAQY
VRVYPERWSPAGIGMRLEVLGCDWT

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 O60462 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TJT 1.31 Å, Neuropilin2-b1 domain in a complex with the C-terminal VEGFC peptide
5DQ0 1.8 Å, Structure of human neuropilin-2 b1 domain with novel and unique zinc binding site
8IVX 1.9 Å, Crystal structure of NRP2 in complex with aNRP2-14 Fab fragment
4QDQ 1.95 Å, Physical basis for Nrp2 ligand binding
5DN2 1.95 Å, Human NRP2 b1 domain in complex with the peptide corresponding to the C-terminus of VEGF-A
2QQO 2.3 Å, Crystal Structure of the a2b1b2 Domains from Human Neuropilin-2
4QDR 2.4 Å, Physical basis for Nrp2 ligand binding
4QDS 2.4 Å, Physical basis for Nrp2 ligand binding
6GH8 2.44 Å, Crystal structure of GP1 domain of Lujo virus in complex with the first CUB domain of…
6TDB 2.45 Å, Neuropilin2-b1 domain in a complex with the C-terminal VEGFB167 peptide
2QQK 2.75 Å, Neuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab
2QQL 3.1 Å, Neuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab

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