5DN2: Human NRP2 b1 domain

Human NRP2 b1 domain in complex with the peptide corresponding to the C-terminus of VEGF-A. Determined by X-ray diffraction at 1.95 Å resolution. Released 20 Jul 2016.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 7
Atoms: 5,504
Mol. weight: 81.76 kDa
Ligands: DIO
Released: 20 Jul 2016

Explore 5DN2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DN2 contains 12 α-helices and 61 β-strands across 5 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: 3 helices, 15 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	421-428	8	1

Chain B: 2 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	279-280	2	5
α-helix	290-292	3
β-strand	293-295	3	5
α-helix	306-308	3
β-strand	310	1	5
β-strand	318	1	6
β-strand	329-345	17	5
β-strand	347-348	2	7
β-strand	355-356	2	7
β-strand	357-366	10	5
β-strand	373-374	2	5
β-strand	376-377	2	8
β-strand	380-381	2	8
β-strand	384-385	2	5
β-strand	394-415	22	5
β-strand	417	1	5
β-strand	420	1	6
β-strand	421-428	8	5

Chains C and D: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	279-280	2	9
α-helix	290-292	3
β-strand	293-295	3	9
α-helix	306-308	3
β-strand	310	1	9
β-strand	318	1	10
β-strand	329-345	17	9
β-strand	347-348	2	11
β-strand	355-356	2	11
β-strand	357-366	10	9
β-strand	373-374	2	9
β-strand	376	1	12
β-strand	381	1	12
α-helix	382	1
β-strand	384-385	2	9
β-strand	394-415	22	9
β-strand	420	1	10
β-strand	421-427	7	9

Chain E: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	228-231	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuropilin-2	A, B, C, D	protein	156	Homo sapiens	O60462 (AlphaFold model)
Vascular endothelial growth factor A	E, F, G	protein	28	Homo sapiens	P15692 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5DN2_1 Neuropilin-2 (chains A, B, C, D)
MFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQVDL
RFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDATEV
VLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRV

Sequence of entity 2 (E, F, G), FASTA

>5DN2_2 Vascular endothelial growth factor A (chains E, F, G)
SCKNTDSRCKARQLELNERTCRCDKPRR

Ligands and cofactors

ID	Name	Formula	Copies
DIO	1,4-diethylene dioxide	C4 H8 O2	2

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

Primary citation

Structural studies of neuropilin-2 reveal a zinc ion binding site remote from the vascular endothelial growth factor binding pocket. Tsai, Y.C., Fotinou, C., Rana, R. et al. FEBS J (2016) 283:1921-1934. DOI 10.1111/febs.13711 · 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
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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