4QDQ: Physical basis for Nrp2 ligand binding

Physical basis for Nrp2 ligand binding. Determined by X-ray diffraction at 1.95 Å resolution. Released 15 Apr 2015.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,444
Mol. weight: 74.9 kDa
Released: 15 Apr 2015

Explore 4QDQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4QDQ contains 14 α-helices and 60 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: 7 helices, 28 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
α-helix	382	1
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	437	1	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	521-529	9	5
β-strand	536-537	2	5
α-helix	538	1
β-strand	539-540	2	7
β-strand	545-546	2	7
β-strand	549-550	2	5
β-strand	559-578	20	5
β-strand	585	1	6
β-strand	586-593	8	5

Chain B: 7 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	279-280	2	8
α-helix	290-292	3
β-strand	293-295	3	8
α-helix	306-308	3
β-strand	310	1	8
β-strand	318	1	9
β-strand	329-345	17	8
β-strand	347-348	2	10
β-strand	355-356	2	10
β-strand	357-366	10	8
β-strand	373-374	2	8
β-strand	376-377	2	11
β-strand	380-381	2	11
α-helix	382-383	2
β-strand	384-385	2	8
β-strand	394-415	22	8
β-strand	420	1	9
β-strand	421-428	8	8
α-helix	429-431	3
β-strand	436-437	2	12
α-helix	447-449	3
β-strand	450-452	3	12
α-helix	462-465	4
β-strand	466	1	12
β-strand	474	1	13
β-strand	488-504	17	12
β-strand	506	1	14
β-strand	519	1	14
β-strand	521-529	9	12
β-strand	536-537	2	12
α-helix	538	1
β-strand	539-540	2	15
β-strand	545-546	2	15
β-strand	549-550	2	12
β-strand	559-578	20	12
β-strand	579	1	16
β-strand	582	1	16
β-strand	585	1	13
β-strand	586-592	7	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuropilin-2	A, B	protein	329	Homo sapiens	O60462 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4QDQ_1 Neuropilin-2 (chains A, B)
GSHMQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQV
DLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDAT
EVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTDAPCSNMLGMLSGLIADSQIS
ASSTQEYLWSPSAARLVSSRSGWFPRIPQAQPGEEWLQVDLGTPKTVKGVIIQGARGGDS
ITAVEARAFVRKFKVSYSLNGKDWEYIQDPRTQQPKLFEGNMHYDTPDIRRFDPIPAQYV
RVYPERWSPAGIGMRLEVLGCDWTSIIRR

Primary citation

Structural Basis for VEGF-C Binding to Neuropilin-2 and Sequestration by a Soluble Splice Form. Parker, M.W., Linkugel, A.D., Goel, H.L. et al. Structure (2015) 23:677-687. DOI 10.1016/j.str.2015.01.018 · 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
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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