2QQO: A2b1b2 Domains from Human Neuropilin-2

Crystal Structure of the a2b1b2 Domains from Human Neuropilin-2. Determined by X-ray diffraction at 2.3 Å resolution. Released 20 Nov 2007.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,212
Mol. weight: 104.45 kDa
Ligands: CA
Released: 20 Nov 2007

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

Secondary structure: helices and β-sheets

2QQO contains 22 α-helices and 74 β-strands across 2 chains. 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: 12 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	151-153	3	1
β-strand	157-161	5	2
α-helix	168-170	3
β-strand	174-180	7	1
α-helix	185	1
β-strand	186-195	10	2
β-strand	212-216	5	1
α-helix	224	1
β-strand	225-229	5	1
α-helix	234-237	4
β-strand	238-240	3	2
β-strand	244-250	7	1
β-strand	259-267	9	2
β-strand	279-280	2	3
α-helix	290-292	3
β-strand	293-295	3	3
α-helix	306-308	3
β-strand	310	1	3
β-strand	318	1	4
β-strand	329-345	17	3
β-strand	347-348	2	5
β-strand	355-356	2	5
β-strand	357-366	10	3
β-strand	373-374	2	3
β-strand	376-377	2	6
β-strand	380-381	2	6
α-helix	382	1
β-strand	384-385	2	3
β-strand	394-415	22	3
β-strand	420	1	4
β-strand	421-427	7	3
α-helix	429-431	3
β-strand	436-437	2	7
α-helix	447-449	3
β-strand	450-452	3	7
α-helix	462-465	4
β-strand	466	1	7
β-strand	474	1	8
β-strand	488-504	17	7
α-helix	515-517	3
β-strand	521-529	9	7
β-strand	536-537	2	7
α-helix	538	1
β-strand	539-540	2	9
β-strand	545-546	2	9
β-strand	549-550	2	7
β-strand	559-578	20	7
β-strand	585	1	8
β-strand	586-593	8	7

Chain B: 10 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	151-153	3	10
β-strand	157-161	5	11
α-helix	168-170	3
β-strand	174-180	7	10
β-strand	186-195	10	11
β-strand	212-216	5	10
α-helix	224	1
β-strand	225-229	5	10
α-helix	234-237	4
β-strand	238-240	3	11
β-strand	244-250	7	10
β-strand	259-267	9	11
β-strand	279-280	2	12
α-helix	290-292	3
β-strand	293-295	3	12
α-helix	306-308	3
β-strand	310	1	12
β-strand	318	1	13
β-strand	329-345	17	12
β-strand	347-348	2	14
β-strand	355-356	2	14
β-strand	357-366	10	12
β-strand	373-374	2	12
β-strand	376-377	2	15
β-strand	380-381	2	15
α-helix	382	1
β-strand	384-385	2	12
β-strand	394-415	22	12
β-strand	420	1	13
β-strand	421-427	7	12
α-helix	429-431	3
β-strand	436-437	2	16
α-helix	447-449	3
β-strand	450-452	3	16
α-helix	462-465	4
β-strand	466	1	16
β-strand	474	1	17
β-strand	488-504	17	16
β-strand	521-529	9	16
β-strand	535-537	3	16
α-helix	538	1
β-strand	539-540	2	18
β-strand	545-546	2	18
β-strand	549-550	2	16
β-strand	559-578	20	16
β-strand	585	1	17
β-strand	586-592	7	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuropilin-2	A, B	protein	460	Homo sapiens	O60462 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2QQO_1 Neuropilin-2 (chains A, B)
ADPGSEDCSKNFTSPNGTIESPGFPEKYPHNLDCTFTILAKPKMEIILQFLIFDLEHDPL
QVGEGDCKYDWLDIWDGIPHVGPLIGKYCGTKTPSELRSSTGILSLTFHTDMAVAKDGFS
ARYYLVHQEPLENFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPN
LDSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNH
KVFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTDAPCSNMLGML
SGLIADSQISASSTQEYLWSPSAARLVSSRSGWFPRIPQAQPGEEWLQVDLGTPKTVKGV
IIQGARGGDSITAVEARAFVRKFKVSYSLNGKDWEYIQDPRTQQPKLFEGNMHYDTPDIR
RFDPIPAQYVRVYPERWSPAGIGMRLEVLGCDWTHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2

Water and common crystallization additives (TRS, 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 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
2QQJ 1.95 Å, Crystal Structure of the b1b2 Domains from Human Neuropilin-2
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
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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