6S2L: Genome polyprotein

FMDV 3D polymerase crystallized in presence of (F)uridylylated VPg peptide. Determined by X-ray diffraction at 2.3 Å resolution. Released 3 Jul 2019.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Foot-and-mouth disease virus (isolate -/Spain/S8c1SantaPau/1970 serotype C)
Chains: 1
Atoms: 3,910
Mol. weight: 54.39 kDa
Released: 3 Jul 2019

Explore 6S2L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6S2L contains 33 α-helices and 24 β-strands across 1 chain. 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: 33 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-13	12	1
β-strand	21-23	3	2
α-helix	25-30	6
β-strand	34-36	3	3
α-helix	37-38	2
α-helix	47	1
α-helix	52-55	4
α-helix	64-67	4
α-helix	68-89	22
α-helix	94-97	4
α-helix	98-103	6
β-strand	105	1	4
β-strand	108	1	4
α-helix	109-112	4
α-helix	128-131	4
β-strand	132-133	2	5
β-strand	138-139	2	5
α-helix	141-151	11
β-strand	159-163	5	1
β-strand	167-169	3	3
α-helix	170-174	5
β-strand	180-183	4	1
α-helix	186-205	20
β-strand	208	1	6
β-strand	213	1	6
α-helix	219-230	12
β-strand	235-238	4	6
β-strand	239-241	3	7
α-helix	250-260	11
α-helix	263-265	3
α-helix	269-276	8
β-strand	280-293	14	1
α-helix	296-297	2
α-helix	301-303	3
α-helix	304-322	19
α-helix	328-330	3
β-strand	332-336	5	6
β-strand	339-344	6	6
α-helix	350-353	4
α-helix	354-358	5
β-strand	364-366	3	7
α-helix	380-382	3
β-strand	385	1	8
β-strand	388-392	5	8
β-strand	399-403	5	8
α-helix	404	1
α-helix	405-413	9
β-strand	414-416	3	2
α-helix	420-431	12
α-helix	432-434	3
α-helix	436-443	8
α-helix	444-446	3
β-strand	447	1	9
β-strand	450	1	9
α-helix	452-454	3
α-helix	455-466	12
α-helix	468-473	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Genome polyprotein	A	protein	481	Foot-and-mouth disease virus (isolate -/Spain/S8c1SantaPau/1970 serotype C)	P03311

Sequence of entity 1 (A), FASTA

>6S2L_1 Genome polyprotein (chains A)
GLIVDTRDVEERVHVMRKTKLAPTVAHGVFNPEFGPAALSNKDPRLNEGVVLDEVIFSKH
KGDTKMSAEDKALFRRCAADYASRLHSVLGTANAPLSIYEAIKGVDGLDAMEPDTAPGLP
WALQGKRRGALIDFENGTVGPEVEAALKLMEKREYKFACQTFLKDEIRPMEKVRAGKTRI
VDVLPVEHILYTRMMIGRFCAQMHSNNGPQIGSAVGCNPDVDWQRFGTHFAQYRNVWDVD
YSAFDANHCSDAMNIMFEEVFRTEFGFHPNAEWILKTLVNTEHAYENKRITVEGGMPSGC
SATSIINTILNNIYVLYALRRHYEGVELDTYTMISYGDDIVVASDYDLDFEALKPHFKSL
GQTITPADKSDKGFVLGHSITDVTFLKRHFHMDYGTGFYKPVMASKTLEAILSFARRGTI
QEKLISVAGLAVHSGPDEYRRLFEPFQGLFEIPSYRSLYLRWVNAVCGDAAAALEHHHHH
H

Primary citation

(F)uridylylated Peptides Linked to VPg1 of Foot-and- Mouth Disease Virus (FMDV): Design, Synthesis and X-Ray Crystallography of the Complexes with FMDV RNA-Dependent RNA Polymerase. de Castro, S., Ferrer-Orta, C., Mills, A. et al. Molecules (2019) 24. DOI 10.3390/molecules24132360 · PubMed

Other PDB entries of the same protein (UniProt P03311), best resolution first:

8C1N 1.7 Å, FMDV 3D polymerase in complex with 3B1 protein solved in P212121 space group
4WYW 1.8 Å, Mutant K20E of 3D polymerase from Foot-and-Mouth Disease Virus
6KWL 1.8 Å, Crystal structure of pSLA-1*0401(R156A) complex with FMDV-derived epitope MTAHITVPY
8C2P 1.85 Å, FMDV 3D polymerase in complex with 3B3
4WYL 2.0 Å, Mutant K18E of 3D polymerase from Foot-and-Moth Disease Virus
6GVY 2.2 Å, Mutant M16A of RNA dependent RNA polymerase 3D from Foot-and-Mouth disease Virus…
6GVV 2.35 Å, Mutant M16A of RNA dependent RNA polymerase 3D from Foot-and-Mouth disease Virus
5N8X 2.4 Å, Trigonal structure of mutant V173I of 3D polymerase from Foot-and-Mouth Disease Virus
6KWK 2.5 Å, Crystal structure of pSLA-1*0401 complex with FMDV-derived epitope MTAHITVPY
9I3H 2.5 Å, CP of RHDV mutant - N15
4WZM 2.52 Å, Mutant K18E of RNA dependent RNA polymerase from Foot-and-Mouth Disease Virus complexed…
5N95 2.6 Å, Tetragonal structure of mutant V173I of 3D polymerase from Foot-and-Mouth Disease Virus

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