2QQL: Neuropilin-2 a1a2b1b2 Domains

Neuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab. Determined by X-ray diffraction at 3.1 Å resolution. Released 20 Nov 2007.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 7,740
Mol. weight: 113.58 kDa
Released: 20 Nov 2007

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

Secondary structure: helices and β-sheets

2QQL contains 26 α-helices and 95 β-strands across 3 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: 11 helices, 50 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	1
β-strand	38-41	4	2
α-helix	48-50	3
β-strand	53-60	8	1
β-strand	67-72	6	2
β-strand	77	1	3
β-strand	87-92	6	1
β-strand	99-104	6	1
α-helix	109-112	4
β-strand	113-114	2	2
β-strand	119-126	8	1
β-strand	134	1	3
β-strand	136-142	7	2
α-helix	143	1
β-strand	147	1	4
β-strand	151-153	3	5
β-strand	157-161	5	6
β-strand	173	1	4
β-strand	174-180	7	5
β-strand	185-195	11	6
β-strand	212-216	5	5
α-helix	224	1
β-strand	225-229	5	5
α-helix	235-237	3
β-strand	238-240	3	6
β-strand	244-250	7	5
β-strand	259-268	10	6
β-strand	279-280	2	7
α-helix	290-292	3
β-strand	293-295	3	7
α-helix	306-308	3
β-strand	310	1	7
β-strand	318	1	8
β-strand	329-345	17	7
β-strand	347-348	2	9
β-strand	355-356	2	9
β-strand	357-366	10	7
β-strand	373-374	2	7
β-strand	376	1	10
β-strand	381	1	10
β-strand	384-385	2	7
β-strand	394-415	22	7
β-strand	420	1	8
β-strand	421-428	8	7
α-helix	429-431	3
β-strand	436-437	2	11
α-helix	447-449	3
β-strand	450-452	3	11
α-helix	462-465	4
β-strand	466	1	11
β-strand	474	1	12
β-strand	488-504	17	11
β-strand	521-529	9	11
β-strand	535-537	3	11
α-helix	538	1
β-strand	539-540	2	13
β-strand	545-546	2	13
β-strand	549-550	2	11
β-strand	559-578	20	11
β-strand	585	1	12
β-strand	586-593	8	11

Chain H: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	14
β-strand	11-12	2	15
β-strand	18-25	8	14
β-strand	33-39	7	16
β-strand	45-51	7	16
β-strand	57-59	3	16
β-strand	67-72	6	14
α-helix	73-75	3
β-strand	77-82	6	14
α-helix	84-86	3
β-strand	88-95	8	16
α-helix	100A-100C	3
β-strand	100G-103	4	16
β-strand	107-109	3	16
β-strand	110-111	2	15
α-helix	115-116	2
β-strand	117	1	17
α-helix	118-119	2
β-strand	120-124	5	18
β-strand	135-145	11	18
β-strand	146	1	17
β-strand	151-154	4	19
α-helix	155-157	3
β-strand	159	1	19
β-strand	163-165	3	18
α-helix	166-168	3
β-strand	169-170	2	18
β-strand	176-185	10	18
β-strand	195-200	6	19
α-helix	201-203	3
β-strand	205-210	6	19
α-helix	211	1

Chain L: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	20
β-strand	10-14	5	21
β-strand	19-25	7	20
β-strand	33-38	6	21
β-strand	45-49	5	21
β-strand	53-54	2	21
α-helix	55	1
β-strand	62-66	5	20
β-strand	70-75	6	20
α-helix	80-82	3
β-strand	84-90	7	21
β-strand	97-98	2	21
β-strand	102-107	6	21
β-strand	111	1	22
α-helix	112-113	2
β-strand	114-115	2	23
β-strand	118	1	23
α-helix	122-127	6
β-strand	129-139	11	23
β-strand	140	1	22
β-strand	145-150	6	24
β-strand	155	1	24
β-strand	159-163	5	23
α-helix	164-167	4
β-strand	173-182	10	23
α-helix	183-186	4
β-strand	191-197	7	24
β-strand	205-210	6	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuropilin-2	A	protein	579	Homo sapiens	O60462 (AlphaFold model)
Antibody Heavy Chain	H	protein	231	Homo sapiens	P01857 (AlphaFold model)
Antibody Light Chain	L	protein	214	Homo sapiens	P01834 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2QQL_1 Neuropilin-2 (chains A)
QPDPPCGGRLNSKDAGYITSPGYPQDYPSHQNCEWIVYAPEPNQKIVLNFNPHFEIEKHD
CKYDFIEIRDGDSESADLLGKHCGNIAPPTIISSGSMLYIKFTSDYARQGAGFSLRYEIF
KTGSEDCSKNFTSPNGTIESPGFPEKYPHNLDCTFTILAKPKMEIILQFLIFDLEHDPLQ
VGEGDCKYDWLDIWDGIPHVGPLIGKYCGTKTPSELRSSTGILSLTFHTDMAVAKDGFSA
RYYLVHQEPLENFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNL
DSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHK
VFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTDAPCSNMLGMLS
GLIADSQISASSTQEYLWSPSAARLVSSRSGWFPRIPQAQPGEEWLQVDLGTPKTVKGVI
IQGARGGDSITAVEARAFVRKFKVSYSLNGKDWEYIQDPRTQQPKLFEGNMHYDTPDIRR
FDPIPAQYVRVYPERWSPAGIGMRLEVLGCDWTHHHHHH

Sequence of entity 2 (H), FASTA

>2QQL_2 Antibody Heavy Chain (chains H)
EVQLVESGGGLVQPGGSLRLSCAASGFTISGYGIHWVRQAPGKGLEWVAYIYPDSGYTDY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCAREDFRNRRRLWYVMDYWGQGTLV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 3 (L), FASTA

>2QQL_3 Antibody Light Chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQAWAYLPTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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
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

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