5VPK: Mite allergen der F 1

Crystal structure of mite allergen der F 1. Determined by X-ray diffraction at 2.0 Å resolution. Released 24 May 2017.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Dermatophagoides farinae
Chains: 3
Atoms: 5,614
Mol. weight: 76.53 kDa
Ligands: NAG
Released: 24 May 2017

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

Secondary structure: helices and β-sheets

5VPK contains 35 α-helices and 54 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, 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
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
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 B: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	2	1
β-strand	3	1	6
α-helix	4	1
β-strand	15-16	2	6
α-helix	17-20	4
β-strand	28	1	7
β-strand	33	1	8
α-helix	35-52	18
β-strand	58	1	9
α-helix	60-62	3
α-helix	63-67	5
β-strand	73	1	8
α-helix	77-87	11
β-strand	89	1	10
β-strand	91	1	9
α-helix	92-94	3
β-strand	112	1	10
β-strand	116-119	4	6
α-helix	125-135	11
α-helix	138	1
β-strand	139-145	7	6
α-helix	148-152	5
β-strand	160	1	6
β-strand	169-181	13	6
β-strand	184-190	7	6
β-strand	193	1	7
β-strand	199	1	6
β-strand	202-206	5	6
α-helix	211-213	3
β-strand	219-222	4	6

Chain C: 12 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	2	1
β-strand	3	1	11
α-helix	4	1
β-strand	15-16	2	11
α-helix	17-20	4
β-strand	28	1	12
β-strand	33	1	13
α-helix	35-52	18
β-strand	58	1	14
α-helix	60-62	3
α-helix	63-67	5
β-strand	73	1	13
α-helix	77-87	11
β-strand	89	1	15
β-strand	91	1	14
α-helix	92-94	3
β-strand	112	1	15
β-strand	117-119	3	11
α-helix	125-135	11
α-helix	138	1
β-strand	139-145	7	11
α-helix	148-152	5
β-strand	160	1	11
β-strand	169-181	13	11
β-strand	184-190	7	11
β-strand	193	1	12
β-strand	199	1	11
β-strand	202-206	5	11
α-helix	211-213	3
β-strand	219-221	3	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Der f 1 variant	A, B, C	protein	223	Dermatophagoides farinae	P16311 (AlphaFold model)

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

>5VPK_1 Der f 1 variant (chains A, B, C)
TSACRINSVNVPSELDLRSLRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNTSLDLSE
QELVDCASQHGCHGDTIPRGIEYIQQNGVVEERSYPYVAREQQCRRPNSQHYGISNYCQI
YPPDVKQIREALTQTHTAIAVIIGIKDLRAFQHYDGRTIIQHDNGYQPNYHAVNIVGYGS
TQGVDYWIVRNSWDTTWGDSGYGYFQAGNNLMMIEQYPYVVIM

Ligands and cofactors

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

Water and common crystallization additives (SO4) are not listed.

Primary citation

Crystal Structures Of Mite Allergens Der F 1 And Der P 1 Reveal Differences In Surface-Exposed Residues That May Influence Antibody Binding. Chruszcz, M., Chapman, M.D., Vailes, L.D. et al. J Mol Biol (2009) 386:520. DOI 10.1016/J.JMB.2008.12.049 · PubMed

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

5VPL 1.9 Å, Crystal structure of der F 1 complexed with FAB 4C1

Browse structure collections

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