6TJT: Neuropilin-2

Neuropilin2-b1 domain in a complex with the C-terminal VEGFC peptide. Determined by X-ray diffraction at 1.31 Å resolution. Released 16 Dec 2020.

Method: X-ray diffraction
Resolution: 1.31 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,955
Mol. weight: 38.84 kDa
Released: 16 Dec 2020

Explore 6TJT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6TJT contains 4 α-helices and 26 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.

Chains A and B: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	280	1	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	373-375	3	1
β-strand	384-385	2	1
β-strand	394-415	22	1
β-strand	420	1	2
β-strand	421-428	8	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuropilin-2	A, B	protein	162	Homo sapiens	O60462 (AlphaFold model)
VEGFC C terminal peptide	D, F	protein	6	Homo sapiens	P49767 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6TJT_1 Neuropilin-2 (chains A, B)
GHMFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQV
DLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDAT
EVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTSGS

Sequence of entity 2 (D, F), FASTA

>6TJT_2 VEGFC C terminal peptide (chains D, F)
XSIIRR

Primary citation

VEGFA, B, C: Implications of the C-Terminal Sequence Variations for the Interaction with Neuropilins. Eldrid, C., Zloh, M., Fotinou, C. et al. Biomolecules (2022) 12. DOI 10.3390/biom12030372 · PubMed

Other PDB entries of the same protein (UniProt O60462 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
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

Browse structure collections

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