5VPL: Der F 1

Crystal structure of der F 1 complexed with FAB 4C1. Determined by X-ray diffraction at 1.9 Å resolution. Released 24 May 2017.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Dermatophagoides farinae, Mus musculus
Chains: 3
Atoms: 5,847
Mol. weight: 77.3 kDa
Ligands: CA, NAG
Released: 24 May 2017

Explore 5VPL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VPL contains 29 α-helices and 62 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: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	2	1
β-strand	3	1	1
α-helix	4	1
β-strand	15-16	2	1
α-helix	17-20	4
α-helix	24-26	3
β-strand	28	1	2
β-strand	33	1	3
α-helix	35-52	18
β-strand	58	1	4
α-helix	60-66	7
β-strand	73	1	3
α-helix	77-87	11
β-strand	89	1	5
β-strand	91	1	4
α-helix	92-94	3
α-helix	103-105	3
β-strand	112	1	5
β-strand	116-119	4	1
α-helix	125-135	11
α-helix	138	1
β-strand	139-145	7	1
α-helix	148-152	5
β-strand	160	1	1
β-strand	169-181	13	1
β-strand	184-190	7	1
β-strand	193	1	2
β-strand	199	1	1
β-strand	202-206	5	1
α-helix	211-213	3
β-strand	219-222	4	1

Chain C: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	33-38	6	7
β-strand	45-49	5	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	84-90	7	7
α-helix	96	1
β-strand	97-98	2	7
β-strand	102-106	5	7
β-strand	111	1	8
α-helix	112-113	2
β-strand	114-118	5	9
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	9
β-strand	140	1	8
β-strand	145-150	6	10
β-strand	153-154	2	10
β-strand	159-163	5	9
α-helix	164-167	4
β-strand	173-182	10	9
α-helix	183-187	5
β-strand	191-197	7	10
β-strand	205-210	6	10

Chain D: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	11-12	2	12
β-strand	18-25	8	11
β-strand	34-40	7	13
β-strand	46-53	8	13
β-strand	58-60	3	13
α-helix	62-64	3
β-strand	68-73	6	11
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-99	8	13
β-strand	110-111	2	13
β-strand	115-117	3	13
β-strand	118-119	2	12
α-helix	123-124	2
β-strand	125	1	14
α-helix	126-127	2
β-strand	128-132	5	15
β-strand	143-153	11	15
β-strand	154	1	14
β-strand	159-162	4	16
α-helix	163-165	3
β-strand	167	1	16
β-strand	171-173	3	15
α-helix	174-176	3
β-strand	177-179	3	15
β-strand	182-192	11	15
α-helix	193-195	3
β-strand	202-207	6	16
α-helix	208-210	3
β-strand	212-217	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Der f 1 variant	A	protein	223	Dermatophagoides farinae	P16311 (AlphaFold model)
4C1 - light chain	C	protein	213	Mus musculus	Q7TS98 (AlphaFold model)
4C1 - heavy chain	D	protein	255	Mus musculus

Sequence of entity 1 (A), FASTA

>5VPL_1 Der f 1 variant (chains A)
TSACRINSVNVPSELDLRSLRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNTSLDLSE
QELVDCASQHGCHGDTIPRGIEYIQQNGVVEERSYPYVAREQQCRRPNSQHYGISNYCQI
YPPDVKQIREALTQTHTAIAVIIGIKDLRAFQHYDGRTIIQHDNGYQPNYHAVNIVGYGS
TQGVDYWIVRNSWDTTWGDSGYGYFQAGNNLMMIEQYPYVVIM

Sequence of entity 2 (C), FASTA

>5VPL_2 4C1 - LIGHT CHAIN (chains C)
QIVMTQSPFSMYATLGERVTITCKASQDIYSYLSWLQQKPGKSLKTLIYRANRLITGVPS
RFSGSGSGQDYSLTISSLEYEDMGIYYCLQYDEFPYTFGGGTKLEMKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Sequence of entity 3 (D), FASTA

>5VPL_3 4C1 - HEAVY CHAIN (chains D)
EVQLQESGPGLVKPSQSLSLTCTVTGYSITSDYAWNWIRQFPGNKLEWMGYISYSGTTSY
NPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYYCGRTGVYRYPERAPYWGQGTLVTVS
AAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQS
DLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCGCKPCICTVPEVSSVFI
FPPKPKDVLTITLTP

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

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

Primary citation

Molecular Determinants For Antibody Binding On Group 1 House Dust Mite Allergens. Chruszcz, M., Pomes, A., Glesner, J. et al. J Biol Chem (2012) 287:7388. DOI 10.1074/JBC.M111.311159 · PubMed

Other PDB entries of the same protein (UniProt P16311 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VPK 2.0 Å, Crystal structure of mite allergen der F 1

Browse structure collections

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