2QQK: Neuropilin-2 a1a2b1b2 Domains

Neuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab. Determined by X-ray diffraction at 2.75 Å resolution. Released 20 Nov 2007.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Homo sapiens
Chains: 3
Atoms: 7,621
Mol. weight: 114.02 kDa
Ligands: NAG
Released: 20 Nov 2007

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

Secondary structure: helices and β-sheets

2QQK contains 27 α-helices and 101 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: 14 helices, 53 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	55-60	6	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	109-111	3
β-strand	113-114	2	2
β-strand	119-125	7	1
β-strand	134	1	3
β-strand	136-142	7	2
β-strand	152-153	2	4
β-strand	157-161	5	5
α-helix	168-170	3
β-strand	174-180	7	4
β-strand	185-195	11	5
β-strand	212-216	5	4
α-helix	224	1
β-strand	225-229	5	4
α-helix	234-237	4
β-strand	238-240	3	5
β-strand	244-250	7	4
β-strand	259-268	10	5
β-strand	279-280	2	6
α-helix	290-292	3
β-strand	293-295	3	6
α-helix	306-308	3
β-strand	310	1	6
β-strand	318	1	7
β-strand	329-345	17	6
β-strand	347-348	2	8
β-strand	355-356	2	8
β-strand	357-366	10	6
β-strand	373-374	2	6
β-strand	376-377	2	9
β-strand	380-381	2	9
α-helix	382-383	2
β-strand	384-385	2	6
β-strand	394-415	22	6
β-strand	417	1	6
β-strand	420	1	7
β-strand	421-427	7	6
α-helix	429-431	3
β-strand	436-437	2	10
α-helix	447-449	3
β-strand	450-452	3	10
α-helix	462-465	4
β-strand	466	1	10
β-strand	474	1	11
β-strand	488-504	17	10
β-strand	506	1	12
β-strand	519	1	12
β-strand	521-529	9	10
β-strand	536-537	2	10
α-helix	538	1
β-strand	539	1	13
α-helix	540	1
β-strand	546	1	13
α-helix	547	1
β-strand	549-550	2	10
β-strand	559-578	20	10
β-strand	579	1	14
β-strand	582	1	14
β-strand	585	1	11
β-strand	586-592	7	10

Chain H: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	15
β-strand	11-12	2	16
β-strand	18-25	8	15
β-strand	33-39	7	17
β-strand	45-52	8	17
β-strand	56-59	4	17
β-strand	67-72	6	15
β-strand	77-82	6	15
α-helix	84-86	3
β-strand	88-95	8	17
α-helix	100A-100C	3
β-strand	100G-103	4	17
β-strand	107-109	3	17
β-strand	110-111	2	16
β-strand	117	1	18
β-strand	120-124	5	19
β-strand	136-145	10	19
β-strand	146	1	18
β-strand	151-154	4	20
α-helix	155-157	3
β-strand	159	1	20
β-strand	163-165	3	19
α-helix	166-168	3
β-strand	169-170	2	19
β-strand	176-184	9	19
α-helix	186-188	3
β-strand	189	1	21
β-strand	192	1	21
β-strand	195-199	5	20
β-strand	200	1	22
α-helix	201-203	3
β-strand	205	1	22
β-strand	208-210	3	20

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	23
β-strand	10-14	5	24
β-strand	19-25	7	23
β-strand	33-38	6	24
β-strand	45-49	5	24
β-strand	53-54	2	24
α-helix	55	1
β-strand	62-67	6	23
β-strand	70-75	6	23
α-helix	80-82	3
β-strand	84-90	7	24
β-strand	97-98	2	24
β-strand	102-107	6	24
β-strand	111	1	25
α-helix	112-113	2
β-strand	114-118	5	26
α-helix	119-121	3
α-helix	122-125	4
β-strand	130-139	10	26
β-strand	140	1	25
β-strand	145-150	6	27
β-strand	153-154	2	27
β-strand	159-163	5	26
α-helix	164-167	4
β-strand	173-181	9	26
α-helix	183-188	6
β-strand	192-197	6	27
β-strand	205-209	5	27

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

>2QQK_1 Neuropilin-2 (chains A)
QPDPPCGGRLNSKDAGYITSPGYPQDYPSHQNCEWIVYAPEPNQKIVLNFNPHFEIEKHD
CKYDFIEIRDGDSESADLLGKHCGNIAPPTIISSGSMLYIKFTSDYARQGAGFSLRYEIF
KTGSEDCSKNFTSPNGTIESPGFPEKYPHNLDCTFTILAKPKMEIILQFLIFDLEHDPLQ
VGEGDCKYDWLDIWDGIPHVGPLIGKYCGTKTPSELRSSTGILSLTFHTDMAVAKDGFSA
RYYLVHQEPLENFQCNVPLGMESGRIANEQISASSTYSDGRWTPQQSRLHGDDNGWTPNL
DSNKEYLQVDLRFLTMLTAIATQGAISRETQNGYYVKSYKLEVSTNGEDWMVYRHGKNHK
VFQANNDATEVVLNKLHAPLLTRFVRIRPQTWHSGIALRLELFGCRVTDAPCSNMLGMLS
GLIADSQISASSTQEYLWSPSAARLVSSRSGWFPRIPQAQPGEEWLQVDLGTPKTVKGVI
IQGARGGDSITAVEARAFVRKFKVSYSLNGKDWEYIQDPRTQQPKLFEGNMHYDTPDIRR
FDPIPAQYVRVYPERWSPAGIGMRLEVLGCDWTHHHHHH

Sequence of entity 2 (H), FASTA

>2QQK_2 Antibody Heavy Chain (chains H)
EVQLVESGGGLVQPGGSLRLSCAASGFTISGYGIHWVRQAPGKGLEWVAYIYPDSGYTDY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCAREDFRNRRRLWYVMDYWGQGTLV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 3 (L), FASTA

>2QQK_3 Antibody Light Chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQAWAYLPTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

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
2QQL 3.1 Å, Neuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab

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