2HWD: Human rhinovirus 1A coat protein

Name: PDB 2HWD: A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A
Published: 1994-09-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A. Determined by X-ray diffraction at 3.8 Å resolution. Released 30 Sept 1994.

Method: X-ray diffraction
Resolution: 3.8 Å
Organism: Human rhinovirus 1A
Chains: 4
Atoms: 6,246
Mol. weight: 92.84 kDa
Ligands: W91
Released: 30 Sept 1994

Explore 2HWD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2HWD contains 26 α-helices and 55 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 1: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	6-10	5
β-strand	16	1	1
α-helix	17-18	2
β-strand	20	1	2
β-strand	34	1	3
α-helix	37-39	3
α-helix	47-50	4
β-strand	56	1	2
β-strand	61	1	1
α-helix	67-71	5
β-strand	75-83	9	4
β-strand	98-99	2	5
α-helix	109-113	5
β-strand	116-133	18	4
β-strand	143-147	5	5
α-helix	153-155	3
α-helix	162-164	3
β-strand	170-173	4	5
α-helix	178-180	3
β-strand	181-184	4	4
β-strand	193-194	2	4
β-strand	200	1	6
β-strand	209	1	6
β-strand	220-223	4	5
β-strand	233-241	9	4
β-strand	243-251	9	4
α-helix	253-255	3
α-helix	278-280	3
β-strand	281	1	7

Chain 2: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	14-17	4	8
β-strand	22-25	4	8
β-strand	32-33	2	9
α-helix	34-36	3
α-helix	41-43	3
β-strand	54	1	10
β-strand	64-65	2	9
β-strand	69-70	2	11
β-strand	77-81	5	12
α-helix	82-85	4
α-helix	92-95	4
β-strand	99-105	7	10
β-strand	106-111	6	9
β-strand	121-128	8	12
β-strand	134	1	13
α-helix	140-143	4
β-strand	154-156	3	12
β-strand	167	1	13
α-helix	183-185	3
β-strand	188-192	5	12
β-strand	198-203	6	9
β-strand	212-213	2	10
β-strand	220-226	7	12
α-helix	229-230	2
β-strand	241-242	2	11
β-strand	243-246	4	9
β-strand	249-256	8	10

Chain 3: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	4
α-helix	30-32	3
β-strand	40	1	4
α-helix	43-47	5
α-helix	50	1
β-strand	51-52	2	3
β-strand	58	1	7
α-helix	59-61	3
α-helix	66-68	3
β-strand	69-72	4	3
β-strand	81-86	6	14
α-helix	100-103	4
β-strand	106-110	5	15
β-strand	113-119	7	3
β-strand	126-134	9	14
β-strand	136	1	16
β-strand	138	1	16
α-helix	139-141	3
α-helix	144-148	5
β-strand	151-156	6	14
β-strand	162-167	6	3
β-strand	176-177	2	15
β-strand	188-198	11	14
β-strand	207-215	9	3
β-strand	220-224	5	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Human rhinovirus 1A coat protein (subunit VP1)	1	protein	287	Human rhinovirus 1A	P23008 (AlphaFold model)
Human rhinovirus 1A coat protein (subunit VP2)	2	protein	263	Human rhinovirus 1A	P23008 (AlphaFold model)
Human rhinovirus 1A coat protein (subunit VP3)	3	protein	238	Human rhinovirus 1A	P23008 (AlphaFold model)
Human rhinovirus 1A coat protein (subunit VP4)	4	protein	44	Human rhinovirus 1A	P23008 (AlphaFold model)

Sequence of entity 1 (1), FASTA

>2HWD_1 HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP1) (chains 1)
NPVENYIDEVLNEVLVVPNIKESHHTTSNSAPLLDAAETGHTSNVQPEDAIETRYVITSQ
TRDEMSIESFLGRSGCVHISRIKVDYTDYNGQDINFTKWKITLQEMAQIRRKFELFTYVR
FDSEITLVPCIAGRGDDIGHIVMQYMYVPPGAPIPSKRNDFSWQSGTNMSIFWQHGQPFP
RFSIPFLSIASAYYMFYDGYDGDNTSSKYGSVVTNDMGTICSRIVTEKQKLSVVITTHIY
HKAKHTKAWCPRPPRAVPYTHSHVTNYMPETGDVTTAIVRRNTITTA

Sequence of entity 2 (2), FASTA

>2HWD_2 HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP2) (chains 2)
SPSVEACGYSDRIMQITRGDSTISSDDVANAVVGYGVWPHYLTPQDATAINKPTQPDTSS
NRFYTLESKHWNGSSKGWWWKLPDALKDMGIFGENMYYHFLGRSGYTVHVQCNASKFHQG
TLLVAMIPEHQLASAKHGSVTAGYKLTHPGEAGRDVSQERDASLRQPSDDSWLNFDGTLL
GNLLIFPHQFINLRSNNSATLIVPYVNAVPMDSMLRHNNWCLVIIPISPLRSETTSSNIV
PITVSISPMCAEFSGARAKNIKQ

Sequence of entity 3 (3), FASTA

>2HWD_3 HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP3) (chains 3)
GLPVYITPGSGQFMTTDDMQSPCALPWYHPTKEISIPGEVKNLIEMCQVDTLIPVNNVGN
NVGNVSMYTVQLGNQTGMAQKVFSIKVDITSTPLATTLIGEIASYYTHWTGSLRFSFMFC
GTANTTLKLLLAYTPPGIDEPTTRKDAMLGTHVVWDVGLQSTISLVVPWVSASHFRLTAD
NKYSMAGYITCWYQTNLVVPPSTPQTADMLCFVSACKDFCLRMARDTDLHIQSGPIEQ

Sequence of entity 4 (4), FASTA

>2HWD_4 HUMAN RHINOVIRUS 1A COAT PROTEIN (SUBUNIT VP4) (chains 4)
GAGVSRQNVGTHSTQNSVSNGSSLNYFNINYFKDAASSGASRLD

Ligands and cofactors

ID	Name	Formula	Copies
W91	5-(3-(2,6-dichloro-4-(4,5-dihydro-2-oxazolyl)phenoxy)propyl)-3-methyl isoxazole	C16 H16 Cl2 N2 O3	1

Primary citation

A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A. Kim, K.H., Willingmann, P., Gong, Z.X. et al. J Mol Biol (1993) 230:206-227. DOI 10.1006/jmbi.1993.1137 · PubMed

Other PDB entries of the same protein (UniProt P23008 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1AYM 2.15 Å, Human rhinovirus 16 coat protein at high resolution
1AYN 2.9 Å, Human rhinovirus 16 coat protein
1R1A 3.2 Å, Crystal structure of human rhinovirus serotype 1A (HRV1A)
2HWE 3.8 Å, A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A
2HWF 3.8 Å, A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A

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