2VXQ: Major grass pollen allergen Phl p 2

Name: PDB 2VXQ: Crystal structure of the major grass pollen allergen Phl p 2 in complex with its specific IgE-Fab
Published: 2009-02-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: allergen

Crystal structure of the major grass pollen allergen Phl p 2 in complex with its specific IgE-Fab. Determined by X-ray diffraction at 1.9 Å resolution. Released 17 Feb 2009.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: PHLEUM PRATENSE, HOMO SAPIENS
Chains: 3
Atoms: 4,491
Mol. weight: 57.25 kDa
Released: 17 Feb 2009

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

Secondary structure: helices and β-sheets

2VXQ contains 20 α-helices and 57 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: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	1
α-helix	9	1
β-strand	13	1	1
β-strand	16-23	8	1
β-strand	28-35	8	2
β-strand	40	1	3
β-strand	42-43	2	2
α-helix	44	1
β-strand	45-46	2	1
α-helix	48-50	3
β-strand	51-55	5	1
α-helix	59-60	2
β-strand	64-70	7	2
β-strand	75-82	8	2
β-strand	91-92	2	1

Chain H: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
β-strand	10-11	2	5
β-strand	17-24	8	4
α-helix	28-30	3
β-strand	32	1	2
β-strand	34-40	7	6
β-strand	46-53	8	6
β-strand	58-60	3	6
α-helix	65-67	3
β-strand	68-73	6	4
β-strand	78-83	6	4
α-helix	88-90	3
β-strand	92-99	8	6
β-strand	104-107	4	6
β-strand	111-113	3	6
β-strand	114-115	2	5
β-strand	120	1	7
α-helix	121-122	2
β-strand	123-130	8	8
β-strand	138-148	11	8
β-strand	149	1	7
β-strand	154-157	4	9
α-helix	158-160	3
β-strand	162	1	9
β-strand	166-168	3	8
α-helix	169-171	3
β-strand	172-173	2	8
β-strand	179-188	10	8
α-helix	189-191	3
β-strand	198-203	6	9
α-helix	204-206	3
β-strand	208-213	6	9

Chain L: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-14	5	11
β-strand	19-25	7	10
β-strand	33-38	6	11
β-strand	45-49	5	11
β-strand	53-54	2	11
α-helix	55	1
β-strand	62-67	6	10
β-strand	70-75	6	10
α-helix	80-82	3
β-strand	84-90	7	11
β-strand	93	1	3
β-strand	98	1	11
β-strand	102-107	6	11
β-strand	111	1	12
α-helix	112-113	2
β-strand	114-118	5	13
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	13
β-strand	140	1	12
β-strand	145-150	6	14
β-strand	153-154	2	14
α-helix	155	1
β-strand	159-163	5	13
α-helix	164-167	4
β-strand	173-182	10	13
α-helix	183-187	5
β-strand	191-197	7	14
β-strand	205-210	6	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pollen allergen phl P 2	A	protein	96	PHLEUM PRATENSE	P43214 (AlphaFold model)
FAB	H	protein	216	HOMO SAPIENS	P01857 (AlphaFold model)
FAB	L	protein	214	HOMO SAPIENS	P01834 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2VXQ_1 POLLEN ALLERGEN PHL P 2 (chains A)
VPKVTFTVEKGSNEKHLAVLVKYEGDTMAEVELREHGSDEWVAMTKGEGGVWTFDSEEPL
QGPFNFRFLTEKGMKNVFDDVVPEKYTIGATYAPEE

Sequence of entity 2 (H), FASTA

>2VXQ_2 FAB (chains H)
VQLLESGPGLVKPAQTLSLSCAVSGGSIRSGGYYWSWIRQHPGKGLEWIGYIYHSGNTYY
NPSLKSRIAMSVDTSENKFSLRLNSVTAADTAVYYCARLDGYTLDIWGQGTLVTVSSSTK
GPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS
LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP

Sequence of entity 3 (L), FASTA

>2VXQ_3 FAB (chains L)
EIEMTQSPSSLSASVGDRVTISCRASQRINTYLNWYQHKPGKAPKLLIYAASSLQSGVPS
RFSGSGYGTDFTLTISSLQPEDFASYYCQESLSASYTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

High-Affinity Ige Recognition of a Conformational Epitope of the Major Respiratory Allergen Phl P 2 as Revealed by X-Ray Crystallography. Padavattan, S., Flicker, S., Schirmer, T. et al. J Immunol (2009) 182:2141. DOI 10.4049/JIMMUNOL.0803018 · PubMed

Other PDB entries of the same protein (UniProt P43214 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1WHO 1.9 Å, Allergen phl P 2
1WHP 3.0 Å, Allergen phl P 2
1BMW A fibronectin type III fold in plant allergens: The solution structure of Phl PII from…

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