6TDB: Neuropilin-2

Neuropilin2-b1 domain in a complex with the C-terminal VEGFB167 peptide. Determined by X-ray diffraction at 2.45 Å resolution. Released 18 Nov 2020.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: Homo sapiens
Chains: 7
Atoms: 5,451
Mol. weight: 75.9 kDa
Ligands: ACE
Released: 18 Nov 2020

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

Secondary structure: helices and β-sheets

6TDB contains 11 α-helices and 61 β-strands across 4 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
α-helix	273-275	3
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	421-428	8	1

Chain B: 3 helices, 15 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
α-helix	382-383	2
β-strand	384-385	2	5
β-strand	394-415	22	5
β-strand	420	1	6
β-strand	421-428	8	5

Chain C: 2 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	376-377	2	12
β-strand	380-381	2	12
β-strand	384-385	2	9
β-strand	394-415	22	9
β-strand	420	1	10
β-strand	421-428	8	9

Chain D: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	279-280	2	13
α-helix	290-292	3
β-strand	293-295	3	13
α-helix	306-308	3
β-strand	310	1	13
β-strand	318	1	14
β-strand	329-345	17	13
β-strand	347-348	2	15
β-strand	355-356	2	15
β-strand	357-366	10	13
β-strand	373-374	2	13
β-strand	376-377	2	16
β-strand	380-381	2	16
α-helix	382	1
β-strand	384-385	2	13
β-strand	394-415	22	13
β-strand	417	1	13
β-strand	420	1	14
β-strand	421-428	8	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuropilin-2	A, B, C, D	protein	162	Homo sapiens	O60462 (AlphaFold model)
C-terminal VEGFB167 peptide	F, J, K	protein	5	Homo sapiens

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

>6TDB_1 Neuropilin-2 (chains A, B, C, D)
GHMFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNLDSNKEYLQV
DLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHKVFQANNDAT
EVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTSGS

Sequence of entity 2 (F, J, K), FASTA

>6TDB_2 C-terminal VEGFB167 peptide (chains F, J, K)
RKLRR

Ligands and cofactors

ID	Name	Formula	Copies
ACE	Acetyl group	C2 H4 O	1

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

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:

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
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…
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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