3VDD: HRV2 capsid

Name: PDB 3VDD: Structure of HRV2 capsid complexed with antiviral compound BTA798
Published: 2012-09-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Structure of HRV2 capsid complexed with antiviral compound BTA798. Determined by X-ray diffraction at 3.2 Å resolution. Released 12 Sept 2012.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Human rhinovirus 2
Chains: 4
Atoms: 6,380
Mol. weight: 95.26 kDa
Ligands: BT8
Released: 12 Sept 2012

Explore 3VDD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3VDD contains 37 α-helices and 62 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 A: 13 helices, 19 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	41-43	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
α-helix	84-85	2
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	167-172	6	6
α-helix	176-178	3
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	249-250	2
β-strand	251	1	8
β-strand	257	1	9
β-strand	277	1	10

Chain B: 14 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	14-17	4	11
β-strand	22-25	4	11
β-strand	28	1	12
β-strand	32-33	2	12
α-helix	34-36	3
α-helix	41-43	3
α-helix	52-53	2
β-strand	54	1	12
α-helix	57-59	3
β-strand	64-65	2	12
β-strand	69-71	3	13
β-strand	78-82	5	14
α-helix	84-86	3
α-helix	90-98	9
β-strand	99-111	13	12
β-strand	118-128	11	14
β-strand	134	1	15
α-helix	144-147	4
α-helix	150-152	3
β-strand	154-155	2	14
α-helix	156	1
α-helix	164-166	3
α-helix	167	1
β-strand	168	1	15
α-helix	169	1
α-helix	172-174	3
β-strand	179	1	8
α-helix	184-186	3
β-strand	189-193	5	14
β-strand	199-204	6	12
β-strand	213-214	2	12
β-strand	218	1	7
β-strand	221-233	13	14
β-strand	240-242	3	13
β-strand	243-256	14	12

Chain C: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
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
β-strand	58	1	10
α-helix	66-68	3
β-strand	69-73	5	3
β-strand	77	1	16
β-strand	81-86	6	17
α-helix	94-96	3
α-helix	98-103	6
β-strand	106-110	5	18
β-strand	113-119	7	3
β-strand	126	1	19
β-strand	128-134	7	17
α-helix	135	1
α-helix	139-141	3
α-helix	144-148	5
β-strand	151-156	6	17
β-strand	162-167	6	3
β-strand	176-177	2	18
β-strand	187-192	6	17
β-strand	195	1	16
β-strand	197	1	19
β-strand	205-214	10	3
β-strand	219-223	5	18
β-strand	236	1	9

Chain D: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	35-37	3
α-helix	40-43	4
β-strand	56	1	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein VP1	A	protein	283	Human rhinovirus 2	P04936 (AlphaFold model)
Protein VP2	B	protein	261	Human rhinovirus 2	P04936 (AlphaFold model)
Protein VP3	C	protein	237	Human rhinovirus 2	P04936 (AlphaFold model)
Protein VP4	D	protein	69	Human rhinovirus 2	P04936 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3VDD_1 Protein VP1 (chains A)
NPVENYIDEVLNEVLVVPNINSSNPTTSNSAPALDAAETGHTSSVQPEDVIETRYVQTSQ
TRDEMSLESFLGRSGCIHESKLEVTLANYNKENFTVWAINLQEMAQIRRKFELFTYTRFD
SEITLVPCISALSQDIGHITMQYMYVPPGAPVPNSRDDYAWQSGTNASVFWQHGQAYPRF
SLPFLSVASAYYMFYDGYDEQDQNYGTANTNNMGSLCSRIVTEKHIHKVHIMTRIYHKAK
HVKAWCPRPPRALEYTRAHRTNFKIEDRSIQTAIVTRPIITTA

Sequence of entity 2 (B), FASTA

>3VDD_2 Protein VP2 (chains B)
SPTVEACGYSDRIIQITRGDSTITSQDVANAIVAYGVWPHYLSSKDASAIDKPSQPDTSS
NRFYTLRSVTWSSSSKGWWWKLPDALKDMGIFGENMFYHYLGRSGYTIHVQCNASKFHQG
TLIVALIPEHQIASALHGNVNVGYNYTHPGETGREVKAETRLNPDLQPTEEYWLNFDGTL
LGNITIFPHQFINLRSNNSATIIAPYVNAVPMDSMRSHNNWSLVIIPICPLETSSAINTI
PITISISPMCAEFSGARAKRQ

Sequence of entity 3 (C), FASTA

>3VDD_3 Protein VP3 (chains C)
GLPVFITPGSGQFLTTDDFQSPCALPWYHPTKEISIPGEVKNLVEICQVDSLVPINNTDT
YINSENMYSVVLQSSINAPDKIFSIRTDVASQPLATTLIGEISSYFTHWTGSLRFSFMFC
GTANTTVKLLLAYTPPGIAEPTTRKDAMLGTHVIWDVGLQSTISMVVPWISASHYRNTSP
GRSTSGYITCWYQTRLVIPPQTPPTARLLCFVSGCKDFCLRMARDTNLHLQSGAIAQ

Sequence of entity 4 (D), FASTA

>3VDD_4 Protein VP4 (chains D)
MGAQVSRQNVGTHSTQNSVSNGSSLNYFNINYFKDAASNGASKLEFTQDPSKFTDPVKDV
LEKGIPTLQ

Ligands and cofactors

ID	Name	Formula	Copies
BT8	3-ethoxy-6-{2-[1-(6-methylpyridazin-3-yl)piperidin-4-yl]ethoxy}-1,2-benzoxazole	C21 H26 N4 O3	1

Primary citation

An Orally Available 3-Ethoxybenzisoxazole Capsid Binder with Clinical Activity against Human Rhinovirus. Feil, S.C., Hamilton, S., Krippner, G.Y. et al. ACS Med Chem Lett (2012) 3:303-307. DOI 10.1021/ml2002955 · 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.
1FPN 2.6 Å, Human rhinovirus serotype 2 (HRV2)
3TN9 3.0 Å, X-ray structure of the HRV2 empty capsid (B-particle)

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