4DCD: Genome polyprotein

1.6A resolution structure of PolioVirus 3C Protease Containing a covalently bound dipeptidyl inhibitor. Determined by X-ray diffraction at 1.69 Å resolution. Released 5 Sept 2012.

Method: X-ray diffraction
Resolution: 1.69 Å
Organism: Human poliovirus 1
Chains: 1
Atoms: 1,555
Mol. weight: 21.44 kDa
Ligands: K36, DTT
Released: 5 Sept 2012

Explore 4DCD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4DCD contains 5 α-helices and 14 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: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	2-14	13
β-strand	15-20	6	1
β-strand	23-31	9	1
β-strand	32	1	2
β-strand	34-38	5	1
α-helix	39-41	3
β-strand	46-49	4	1
β-strand	52-63	12	1
β-strand	69-77	9	1
β-strand	83	1	2
α-helix	87-89	3
β-strand	97-104	8	3
β-strand	112-127	16	3
β-strand	130-138	9	3
α-helix	149	1
β-strand	150-153	4	3
β-strand	156-164	9	3
β-strand	169-173	5	3
α-helix	176-179	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Genome polyprotein	A	protein	190	Human poliovirus 1	P03300 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4DCD_1 Genome polyprotein (chains A)
MHHHHHHGPGFDYAVAMAKRNIVTATTSKGEFTMLGVHDNVAILPTHASPGESIVIDGKE
VEILDAKALEDQAGTNLEITIITLKRNEKFRDIRPHIPTQITETNDGVLIVNTSKYPNMY
VPVGAVTEQGYLNLGGRQTARTLMYNFPTRAGQCGGVITCTGKVIGMHVGGNGSHGFAAA
LKRSYFTQSQ

Ligands and cofactors

ID	Name	Formula	Copies
K36	(1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrr…	C21 H31 N3 O8 S	1
DTT	2,3-dihydroxy-1,4-dithiobutane	C4 H10 O2 S2	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Broad-Spectrum Antivirals against 3C or 3C-Like Proteases of Picornaviruses, Noroviruses, and Coronaviruses. Kim, Y., Lovell, S., Tiew, K.C. et al. J Virol (2012) 86:11754-11762. DOI 10.1128/JVI.01348-12 · PubMed

Other PDB entries of the same protein (UniProt P03300 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9U04 1.7 Å, LX-2D6 (Fab) - Polio 1 (VLP) complex
1RA6 2.0 Å, Poliovirus Polymerase Full Length Apo Structure
4NLR 2.0 Å, Poliovirus Polymerase - C290S Loop Mutant
4NLS 2.0 Å, Poliovirus Polymerase - S288A Loop Mutant
1L1N 2.1 Å, Poliovirus 3C proteinase
4NLU 2.1 Å, Poliovirus Polymerase - G289A Loop Mutant
4NLW 2.1 Å, Poliovirus Polymerase - G289A/C290I Loop Mutant
1HXS 2.2 Å, Crystal structure of mahoney strain of poliovirus at 2.2A resolution
4NLO 2.2 Å, Poliovirus Polymerase - C290I Loop Mutant
4NLP 2.2 Å, Poliovirus Polymerase - C290V Loop Mutant
2IM0 2.25 Å, Crystal structure of poliovirus polymerase complexed with CTP and Mg2+
1TQL 2.3 Å, Poliovirus polymerase G1A mutant

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