7QB5: Coxsackievirus A24v

Name: PDB 7QB5: Coxsackievirus A24v (CVA24v) in complex with a dimeric C2-C9-linked sialic acid inhibitor
Published: 2022-05-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Coxsackievirus A24v (CVA24v) in complex with a dimeric C2-C9-linked sialic acid inhibitor. Determined by X-ray diffraction at 1.73 Å resolution. Released 18 May 2022.

Method: X-ray diffraction
Resolution: 1.73 Å
Organism: Coxsackievirus A24
Chains: 4
Atoms: 7,489
Mol. weight: 98.88 kDa
Ligands: CA, HEZ, SIA
Released: 18 May 2022

Explore 7QB5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7QB5 contains 44 α-helices and 64 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 111: 17 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	608-609	2
β-strand	610	1	1
α-helix	611-612	2
β-strand	613	1	2
β-strand	624-625	2	3
α-helix	627-629	3
α-helix	631-633	3
α-helix	637-639	3
β-strand	643	1	2
β-strand	646	1	1
α-helix	653-655	3
β-strand	656	1	4
α-helix	657-661	5
β-strand	665-674	10	5
α-helix	680-683	4
α-helix	684-686	3
β-strand	687-691	5	6
α-helix	699-704	6
β-strand	707-724	18	5
α-helix	733-735	3
β-strand	736-742	7	6
α-helix	747-749	3
α-helix	755-758	4
β-strand	764-768	5	6
β-strand	775-778	4	5
β-strand	787-788	2	5
β-strand	793	1	7
β-strand	799	1	8
α-helix	813-815	3
β-strand	821-826	6	6
α-helix	829-831	3
β-strand	835-853	19	5
α-helix	855-857	3
α-helix	877-878	2
β-strand	879	1	9
β-strand	883	1	10

Chain 222: 14 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	83-87	5	11
β-strand	90-94	5	11
β-strand	101-102	2	12
α-helix	103-105	3
α-helix	110-112	3
α-helix	113-115	3
α-helix	121-122	2
β-strand	123	1	12
α-helix	126-128	3
β-strand	133-134	2	12
α-helix	135-137	3
β-strand	138-140	3	13
β-strand	147-151	5	14
α-helix	153-155	3
α-helix	159-167	9
β-strand	168-180	13	12
β-strand	188-197	10	14
β-strand	203	1	15
β-strand	205	1	16
α-helix	214-217	4
α-helix	220-222	3
β-strand	224-225	2	14
β-strand	227	1	17
β-strand	233	1	16
α-helix	236-238	3
β-strand	242	1	15
β-strand	245	1	17
α-helix	246-248	3
α-helix	255-260	6
β-strand	263-267	5	14
β-strand	273-278	6	12
β-strand	287	1	12
β-strand	292	1	7
β-strand	295-306	12	14
β-strand	315-317	3	13
β-strand	318-331	14	12
α-helix	334-335	2
β-strand	337	1	8

Chain 333: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	346-347	2
β-strand	363	1	5
α-helix	370-373	4
β-strand	379-380	2	5
β-strand	382	1	4
α-helix	383-387	5
β-strand	391-392	2	3
β-strand	398	1	9
α-helix	405-407	3
α-helix	409	1
β-strand	410-413	4	3
β-strand	422-425	4	10
α-helix	438-443	6
β-strand	446-450	5	18
β-strand	453-459	7	3
β-strand	466	1	19
β-strand	468-474	7	10
α-helix	479-481	3
α-helix	484-487	4
β-strand	491-496	6	10
α-helix	497	1
β-strand	502-507	6	3
β-strand	516-517	2	18
β-strand	528-533	6	10
β-strand	538	1	19
β-strand	546-555	10	3
β-strand	560-564	5	18

Chain 444: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	20
α-helix	8-10	3
β-strand	26-29	4	20
α-helix	36-38	3
α-helix	41-44	4
α-helix	51-54	4
β-strand	57	1	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein VP1	111	protein	305	Coxsackievirus A24	V9VEF3
Capsid protein VP2	222	protein	271	Coxsackievirus A24	V9VEF3
Capsid protein VP3	333	protein	240	Coxsackievirus A24	V9VEF3
Capsid protein VP4	444	protein	69	Coxsackievirus A24	V9VEF3

Sequence of entity 1 (111), FASTA

>7QB5_1 Capsid protein VP1 (chains 111)
GIEETIDTVITNALQLSQPKPQKQPTAQSTPLTSGVNSQEVPALTAVETGASGQAVPSDV
IETRHVVNYKTRSESTLESFFGRSACVTILEVENFNATTDADRKKQFTTWAITYTDTVQL
RRKLEFFTYSRFDLEMTFVITERYYASNTGHARNQVYQLMYIPPGAPRPTAWDDYTWQSS
SNPSVFYTYGSAPPRMSIPYVGIANAYSHFYDGFARVPLKDETVDSGDTYYGLVTINDFG
TLAVRVVNEYNPARITSKIRVYMKPKHVRCWCPRPPRAVPYRGEGVDFKQDSITPLTAVE
NINTF

Sequence of entity 2 (222), FASTA

>7QB5_2 Capsid protein VP2 (chains 222)
SPNVEACGYSDRVRQITLGNSTITTQEAANAVVAYGEWPSYLDDKEANPIDAPTEPDVSS
NRFYTLDSVQWKSTSRGWWWKLPDALKDMGMFGQNMYYHYLGRSGYTVHVQCNASKFHQG
ALGVFAIPEYVMACNTEAKTSYVSYVNANPGEKGGVFDNAYNPSAEASEGRKFAALDYLL
GCGVLAGNAFVYPHQIINLRTNNSATLVLPYVNSLAIDCMAKHNNWGLVILPLCKLDYAP
NSSTEIPITVTIAPMFTEFNGLRNITVPATQ

Sequence of entity 3 (333), FASTA

>7QB5_3 Capsid protein VP3 (chains 333)
GLPTMLTPGSSQFLTSDDFQSPCALPNFDVTPPIHIPGEVFNMMELAEIDSMIPMNSVTG
KANTMEMYPIPLDDKGSATPIFSISLSPASDKRLQYTMLGEILNYYTHWTGSLRFTFLFC
GSMMATGKILLSYSPPGAKPPTTRKDAMLGTHIIWDLGLQSSCTMLAPWISNTVYRRCIK
DDFTEGGYITCFYQTRIVVPSGTPTSMFMLAFVSACPDFSVRLLRDTNHISQRTLFARAQ

Sequence of entity 4 (444), FASTA

>7QB5_4 Capsid protein VP4 (chains 444)
MGAQVSSQKVGAHENTNVATGGSTVNYTTINYYKDSASNAASKLDFSQDPSKFTEPVKDI
MIKTAPALN

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4
HEZ	Hexane-1,6-diol	C6 H14 O2	1
SIA	N-acetyl-alpha-neuraminic acid	C11 H19 N O9	1

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

Primary citation

Exploring divalent conjugates of 5- N -acetyl-neuraminic acid as inhibitors of coxsackievirus A24 variant (CVA24v) transduction. Johansson, E., Caraballo, R., Zocher, G. et al. RSC Adv (2022) 12:2319-2331. DOI 10.1039/d1ra08968d · PubMed

Other PDB entries of the same protein (UniProt V9VEF3), best resolution first:

4Q4W 1.4 Å, High-resolution crystal structure of Coxsackievirus A24v
4Q4X 1.65 Å, Crystal structure of Coxsackievirus A24v soaked with 6'-Sialyllactose (6SL)
7OJ7 1.78 Å, Crystal structure of human coxsackievirus A24v in complex with a pentavalent…
6TSD 1.81 Å, Crystal structure of human coxsackievirus A24v in complex with pentavalent inhibitor…
4Q4Y 1.88 Å, Crystal structure of Coxsackievirus A24v soaked with Disialyllacto-N-tetraose (DSLNT)
4Q4V 2.9 Å, Crystal structure of Coxsackievirus A24v
6EIT 3.9 Å, Coxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1

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