1FPN: Human rhinovirus serotype 2

Name: PDB 1FPN: Human rhinovirus serotype 2 (HRV2)
Published: 2000-09-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Human rhinovirus serotype 2 (HRV2). Determined by X-ray diffraction at 2.6 Å resolution. Released 20 Sept 2000.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Human rhinovirus 2
Chains: 4
Atoms: 6,316
Mol. weight: 95.6 kDa
Ligands: DAO
Released: 20 Sept 2000

Explore 1FPN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1FPN contains 36 α-helices and 56 β-strands across 4 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 1: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	1
α-helix	17-19	3
β-strand	20	1	2
α-helix	21-22	2
β-strand	34-35	2	3
α-helix	37-39	3
α-helix	47-50	4
β-strand	56	1	2
β-strand	61	1	1
α-helix	63-65	3
β-strand	66	1	4
α-helix	67-71	5
β-strand	75-83	9	5
β-strand	94-98	5	6
α-helix	105-111	7
β-strand	114-131	18	5
β-strand	140-146	7	6
α-helix	151-153	3
α-helix	159-162	4
β-strand	168-172	5	6
α-helix	175-178	4
β-strand	179-182	4	5
β-strand	191-192	2	5
β-strand	197	1	7
β-strand	215-220	6	6
β-strand	229-247	19	5
α-helix	249-251	3
β-strand	257	1	8

Chain 2: 15 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	14-17	4	9
β-strand	22-25	4	9
β-strand	32-33	2	10
α-helix	34-36	3
α-helix	41-43	3
α-helix	52-53	2
β-strand	54	1	10
α-helix	57-59	3
β-strand	64-65	2	10
α-helix	66-68	3
β-strand	69-71	3	11
β-strand	78-82	5	12
α-helix	84-86	3
α-helix	90-98	9
β-strand	99-111	13	10
β-strand	118-128	11	12
α-helix	132-133	2
β-strand	134	1	13
α-helix	144-147	4
α-helix	150-152	3
β-strand	154-155	2	12
α-helix	167	1
β-strand	168	1	13
α-helix	169	1
α-helix	172-174	3
α-helix	184-186	3
β-strand	189-193	5	12
β-strand	199-204	6	10
β-strand	213	1	10
β-strand	218	1	7
β-strand	221-233	13	12
β-strand	240-242	3	11
β-strand	243-256	14	10
α-helix	259-260	2

Chain 3: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	23	1	5
α-helix	30-33	4
β-strand	39-40	2	5
β-strand	42	1	4
α-helix	44-47	4
β-strand	51-52	2	3
α-helix	65-68	4
β-strand	69-73	5	3
β-strand	81-86	6	14
α-helix	94-96	3
α-helix	98-103	6
β-strand	106-110	5	15
β-strand	113-119	7	3
β-strand	126	1	16
β-strand	127-134	8	14
α-helix	139-141	3
α-helix	144-148	5
β-strand	151-157	7	14
β-strand	162-167	6	3
β-strand	176-177	2	15
β-strand	187-192	6	14
β-strand	197	1	16
β-strand	205-214	10	3
β-strand	219-223	5	15
β-strand	236	1	8

Chain 4: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	17
β-strand	26-27	2	17
α-helix	35-37	3
α-helix	41-42	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coat protein VP1	1	protein	289	Human rhinovirus 2	P04936 (AlphaFold model)
Coat protein VP2	2	protein	261	Human rhinovirus 2	P04936 (AlphaFold model)
Coat protein VP3	3	protein	237	Human rhinovirus 2	P04936 (AlphaFold model)
Coat protein VP4	4	protein	68	Human rhinovirus 2	P04936 (AlphaFold model)

Sequence of entity 1 (1), FASTA

>1FPN_1 COAT PROTEIN VP1 (chains 1)
NPVENYIDEVLNEVLVVPNINSSNPTTSNSAPALDAAETGHTSSVQPEDVIETRYVQTSQ
TRDEMSLESFLGRSGCIHESKLEVTLANYNKENFTVWAINLQEMAQIRRKFELFTYTRFD
SEITLVPCISALSQDIGHITMQYMYVPPGAPVPNSRDDYAWQSGTNASVFWQHGQAYPRF
SLPFLSVASAYYMFYDGYDEQDQNYGTANTNNMGSLCSRIVTEKHIHKVHIMTRIYHKAK
HVKAWCPRPPRALEYTRAHRTNFKIEDRSIQTAIVTRPIITTAGPSDMY

Sequence of entity 2 (2), FASTA

>1FPN_2 COAT PROTEIN VP2 (chains 2)
SPTVEACGYSDRIIQITRGDSTITSQDVANAIVAYGVWPHYLSSKDASAIDKPSQPDTSS
NRFYTLRSVTWSSSSKGWWWKLPDALKDMGIFGENMFYHYLGRSGYTIHVQCNASKFHQG
TLIVALIPEHQIASALHGNVNVGYNYTHPGETGREVKAETRLNPDLQPTEEYWLNFDGTL
LGNITIFPHQFINLRSNNSATIIAPYVNAVPMDSMRSHNNWSLVIIPICPLETSSAINTI
PITISISPMCAEFSGARAKRQ

Sequence of entity 3 (3), FASTA

>1FPN_3 COAT PROTEIN VP3 (chains 3)
GLPVFITPGSGQFLTTDDFQSPCALPWYHPTKEISIPGEVKNLVEICQVDSLVPINNTDT
YINSENMYSVVLQSSINAPDKIFSIRTDVASQPLATTLIGEISSYFTHWTGSLRFSFMFC
GTANTTVKLLLAYTPPGIAEPTTRKDAMLGTHVIWDVGLQSTISMVVPWISASHYRNTSP
GRSTSGYITCWYQTRLVIPPQTPPTARLLCFVSGCKDFCLRMARDTNLHLQSGAIAQ

Sequence of entity 4 (4), FASTA

>1FPN_4 COAT PROTEIN VP4 (chains 4)
GAQVSRQNVGTHSTQNSVSNGSSLNYFNINYFKDAASNGASKLEFTQDPSKFTDPVKDVL
EKGIPTLQ

Ligands and cofactors

ID	Name	Formula	Copies
DAO	Lauric acid	C12 H24 O2	1

Primary citation

Structure of human rhinovirus serotype 2 (HRV2). Verdaguer, N., Blaas, D., Fita, I. J Mol Biol (2000) 300:1179-1194. DOI 10.1006/jmbi.2000.3943 · PubMed

Other PDB entries of the same protein (UniProt P04936 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5FX6 1.45 Å, Novel inhibitors of human rhinovirus 3C protease
5FX5 1.7 Å, Novel inhibitors of human rhinovirus 3C protease
6FFN 1.75 Å, Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease…
9W3O 1.76 Å, Crystal Structure of Human rhinovirus A2 3C Protease in Complex with a Broad-spectrum…
1CQQ 1.85 Å, Type 2 rhinovirus 3C protease with AG7088 inhibitor
6FFS 1.86 Å, Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease…
2HRV 1.95 Å, 2A cysteine proteinase from human rhinovirus 2
1A3R 2.1 Å, FAB fragment (antibody 8F5) complexed with peptide from human rhinovirus (serotype 2)…
7ARA 2.24 Å, Rhinovirus A2 2A protease in complex with zVAM.fmk
2XYA 2.4 Å, Non-covalent inhibtors of rhinovirus 3C protease.
3TN9 3.0 Å, X-ray structure of the HRV2 empty capsid (B-particle)
3VDD 3.2 Å, Structure of HRV2 capsid complexed with antiviral compound BTA798

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