5FFM: Yellow fever virus helicase

Yellow fever virus helicase. Determined by X-ray diffraction at 2.6 Å resolution. Released 30 Dec 2015.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Yellow fever virus (strain 17D vaccine)
Chains: 1
Atoms: 3,314
Mol. weight: 50.01 kDa
Released: 30 Dec 2015

Explore 5FFM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5FFM contains 21 α-helices and 20 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: 21 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	193-196	4	1
α-helix	198-200	3
α-helix	208-219	12
β-strand	223-227	5	1
α-helix	230-239	10
β-strand	245-247	3	1
β-strand	262-266	5	1
α-helix	267-274	8
β-strand	285-289	5	1
α-helix	296-310	15
β-strand	315-319	5	1
β-strand	337-341	5	2
α-helix	354-358	5
β-strand	363-366	4	2
α-helix	370-382	13
β-strand	387-389	3	2
β-strand	409-412	4	2
β-strand	426-429	4	2
β-strand	432-439	8	3
β-strand	444-452	9	3
α-helix	455-462	8
β-strand	474-478	5	2
β-strand	489	1	3
α-helix	490-499	10
α-helix	505-507	3
α-helix	511-512	2
α-helix	516-519	4
α-helix	531-544	14
α-helix	548-557	10
α-helix	565-567	3
α-helix	572-574	3
β-strand	577	1	4
α-helix	582	1
β-strand	583	1	4
α-helix	584	1
β-strand	585-587	3	5
α-helix	588	1
β-strand	593-595	3	5
β-strand	602	1	3
α-helix	603-606	4
α-helix	609-620	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine protease NS3	A	protein	440	Yellow fever virus (strain 17D vaccine)	P03314 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5FFM_1 Serine protease NS3 (chains A)
GSHMLKKGMTTVLDFHPGAGKTRRFLPQILAECARRRLRTLVLAPTRVVLSEMKEAFHGL
DVKFHTQAFSAHGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFLDPASIAARG
WAAHRARANESATILMTATPPGTSDEFPHSNGEIEDVQTDIPSEPWNTGHDWILADKRPT
AWFLPSIRAANVMAASLRKAGKSVVVLNRKTFEREYPTIKQKKPDFILATDIAEMGANLC
VERVLDCRTAFKPVLVDEGRKVAIKGPLRISASSAAQRRGRIGRNPNRDGDSYYYSEPTS
ENNAHHVCWLEASMLLDNMEVRGGMVAPLYGVEGTKTPVSPGEMRLRDDQRKVFRELVRN
CDLPVWLSWQVAKAGLKTNDRKWCFEGPEEHEILNDSGETVKCRAPGGAKKPLRPRWCDE
RVSSDQSALSEFIKFAEGRR

Primary citation

Structure of the Flavivirus helicase: implications for catalytic activity, protein interactions, and proteolytic processing. Wu, J., Bera, A.K., Kuhn, R.J. et al. J Virol (2005) 79:10268-10277. PubMed

Other PDB entries of the same protein (UniProt P03314 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3EVF 1.45 Å, Crystal structure of Me7-GpppA complex of yellow fever virus methyltransferase and…
9SKO 1.49 Å, Crystal structure of HLA-A0201 in complex with peptide LLWNGPMAVS
3EVA 1.5 Å, Crystal structure of yellow fever virus methyltransferase complexed with…
3EVD 1.5 Å, Crystal structure of GTP complex of yellow fever virus methyltransferase and…
3EVC 1.6 Å, Crystal structure of GTP complex of yellow fever virus methyltransferase and…
3EVE 1.7 Å, Crystal structure of GpppA complex of yellow fever virus methyltransferase and…
5N6B 1.71 Å, Human Leukocyte Antigen Class I A02 Carrying LLWNPGMAV
1YKS 1.8 Å, Crystal structure of yellow fever virus NS3 helicase
3EVB 1.85 Å, Crystal structure of yellow fever virus methyltransferase complexed with…
9SKP 1.89 Å, Crystal structure of HLA-A0201 in complex with peptide SLLWNGPMAV
6SSA 2.11 Å, Human Leukocyte Antigen Class I A02 Carrying LLWNGPMQV
6SS8 2.24 Å, Human Leukocyte Antigen Class I A02 Carrying LLWNGPIAV

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