1NCQ: HRV14 when

Name: PDB 1NCQ: The structure of HRV14 when complexed with pleconaril, an antiviral compound
Published: 2003-12-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

The structure of HRV14 when complexed with pleconaril, an antiviral compound. Determined by X-ray diffraction at 2.5 Å resolution. Released 16 Dec 2003.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Human rhinovirus 14
Chains: 4
Atoms: 6,537
Mol. weight: 94.86 kDa
Ligands: W11
Released: 16 Dec 2003

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

Secondary structure: helices and β-sheets

1NCQ contains 39 α-helices and 57 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: 14 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	18-20	3	1
β-strand	23	1	2
β-strand	34-35	2	3
α-helix	37-39	3
α-helix	47-49	3
β-strand	53	1	2
β-strand	56-57	2	1
α-helix	63-65	3
β-strand	66	1	4
α-helix	67-70	4
β-strand	75-84	10	5
α-helix	93-96	4
β-strand	99-103	5	6
α-helix	110-116	7
β-strand	119-135	17	5
β-strand	147-153	7	6
α-helix	158-160	3
α-helix	166-169	4
β-strand	175-179	5	6
β-strand	183-188	6	5
β-strand	197-198	2	5
β-strand	203	1	7
α-helix	215-217	3
β-strand	223-228	6	6
α-helix	231-232	2
β-strand	237-255	19	5
α-helix	257-258	2
β-strand	259	1	8
α-helix	262-263	2
α-helix	275-277	3
α-helix	280-282	3

Chain B: 13 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	14-18	5	9
β-strand	21-25	5	9
β-strand	32-33	2	10
α-helix	34-36	3
α-helix	41-43	3
α-helix	44-46	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	69-72	4	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	119-128	10	12
β-strand	134	1	13
α-helix	144-147	4
α-helix	150-152	3
β-strand	154-155	2	12
α-helix	159-160	2
β-strand	165	1	13
α-helix	169-171	3
β-strand	176	1	8
α-helix	178-183	6
β-strand	186-190	5	12
β-strand	196-201	6	10
β-strand	210	1	10
β-strand	215	1	7
β-strand	218-229	12	12
β-strand	237-240	4	11
β-strand	241-254	14	10

Chain C: 10 helices, 19 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	43-46	4
β-strand	51-52	2	3
α-helix	64-67	4
β-strand	68-71	4	3
β-strand	73	1	14
β-strand	79-84	6	15
α-helix	90-94	5
α-helix	96-101	6
β-strand	104-108	5	16
β-strand	111-117	7	3
β-strand	124	1	17
β-strand	126-132	7	15
α-helix	137-139	3
α-helix	142-146	5
β-strand	149-154	6	15
α-helix	155	1
β-strand	160-165	6	3
β-strand	174-175	2	16
β-strand	186-191	6	15
β-strand	195	1	14
β-strand	196	1	17
α-helix	197-198	2
β-strand	205-213	9	3
β-strand	218-222	5	16

Chain D: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	35-37	3
α-helix	50-53	4
β-strand	56	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coat protein VP1	A	protein	289	Human rhinovirus 14	P03303 (AlphaFold model)
Coat protein VP2	B	protein	262	Human rhinovirus 14	P03303 (AlphaFold model)
Coat protein VP3	C	protein	236	Human rhinovirus 14	P03303 (AlphaFold model)
Coat protein VP4	D	protein	68	Human rhinovirus 14	P03303 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1NCQ_1 COAT PROTEIN VP1 (chains A)
GLGDELEEVIVEKTKQTVASISSGPKHTQKVPILTANETGATMPVLPSDSIETRTTYMHF
NGSETDVECFLGRAACVHVTEIQNKDATGIDNHREAKLFNDWKINLSSLVQLRKKLELFT
YVRFDSEYTILATASQPDSANYSSNLVVQAMYVPPGAPNPKEWDDYTWQSASNPSVFFKV
GDTSRFSVPYVGLASAYNCFYDGYSHDDAETQYGITVLNHMGSMAFRIVNEHDEHKTLVK
IRVYHRAKHVEAWIPRAPRALPYTSIGRTNYPKNTEPVIKKRKGDIKSY

Sequence of entity 2 (B), FASTA

>1NCQ_2 COAT PROTEIN VP2 (chains B)
SPNVEACGYSDRVQQITLGNSTITTQEAANAVVCYAEWPEYLPDVDASDVNKTSKPDTSV
CRFYTLDSKTWTTGSKGWCWKLPDALKDMGVFGQNMFFHSLGRSGYTVHVQCNATKFHSG
CLLVVVIPEHQLASHEGGNVSVKYTFTHPGERGIDLSSANEVGGPVKDVLYNMNGTLLGN
LLIFPHQFINLRTNNTATIVIPYINSVPIDSMTRHNNVSLMVIPIAPLTVPTGATPSLPI
TVTIAPMCTEFSGIRSKSIVPQ

Sequence of entity 3 (C), FASTA

>1NCQ_3 COAT PROTEIN VP3 (chains C)
GLPTTTLPGSGQFLTTDDRQSPSALPNYEPTPRIHIPGKVHNLLEIIQVDTLIPMNNTHT
KDEVNSYLIPLNANRQNEQVFGTNLFIGDGVFKTTLLGEIVQYYTHWSGSLRFSLMYTGP
ALSSAKLILAYTPPGARGPQDRREAMLGTHVVWDIGLQSTIVMTIPWTSGVQFRYTDPDT
YTSAGFLSCWYQTSLILPPETTGQVYLLSFISACPDFKLRLMKDTQTISQTVALTE

Sequence of entity 4 (D), FASTA

>1NCQ_4 COAT PROTEIN VP4 (chains D)
GAQVSTQKSGSHENQNILTNGSNQTFTVINYYKDAASTSSAGQSLSMDPSKFTEPVKDLM
LKGAPALN

Ligands and cofactors

ID	Name	Formula	Copies
W11	3-{3,5-dimethyl-4-[3-(3-methyl-isoxazol-5-yl)-propoxy]-phenyl}-5-trifluoromethy…	C18 H18 F3 N3 O3	1

Primary citation

Structural and virological studies of the stages of virus replication that are affected by antirhinovirus compounds. Zhang, Y., Simpson, A.A., Ledford, R.M. et al. J Virol (2004) 78:11061-11069. DOI 10.1128/JVI.78.20.11061-11069.2004 · PubMed

Other PDB entries of the same protein (UniProt P03303 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KYZ 1.84 Å, HRV14 3C in complex with single chain antibody YDF
9LGP 2.11 Å, Crystal structure of the HRV B14 3C protease in complex with AG7404
5W3M 2.26 Å, CryoEM structure of rhinovirus B14 in complex with C5 Fab (33 degrees Celsius, molar…
6KZ0 2.4 Å, HRV14 3C in complex with single chain antibody GGVV
7BG7 2.4 Å, HRV14 in complex with its receptor ICAM-1
5W3E 2.53 Å, CryoEM structure of rhinovirus B14 in complex with C5 Fab (33 degrees Celsius, molar…
7BG6 2.6 Å, HRV14 native particle solved by cryoEM
31LE 2.64 Å, HRV E1007A mutant
1K5M 2.7 Å, Crystal Structure of a Human Rhinovirus Type 14:Human Immunodeficiency Virus Type 1 V3…
31LF 2.71 Å, HRV virion E2250A mutant
5W3L 2.71 Å, CryoEM structure of rhinovirus B14 in complex with C5 Fab (4 degrees Celsius, molar…
29UB 2.73 Å, HRV B14 virion

Browse structure collections

About this viewer

MolViewer shows 1NCQ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.