4IBD: Ebola virus VP35

Ebola virus VP35 bound to small molecule. Determined by X-ray diffraction at 1.84 Å resolution. Released 19 Mar 2014.

Method: X-ray diffraction
Resolution: 1.84 Å
Organism: Ebola virus
Chains: 2
Atoms: 2,283
Mol. weight: 29.63 kDa
Ligands: MG, 1DL
Released: 19 Mar 2014

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

Secondary structure: helices and β-sheets

4IBD contains 19 α-helices and 8 β-strands across 2 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: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	221-229	9
α-helix	238-252	15
α-helix	256-268	13
α-helix	273-283	11
α-helix	285-287	3
α-helix	290-293	4
β-strand	294-297	4	1
α-helix	300-302	3
α-helix	305-310	6
β-strand	311-312	2	1
α-helix	320-322	3
β-strand	324-330	7	1
β-strand	335-339	5	1

Chain B: 10 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	218-220	3
α-helix	221-231	11
α-helix	238-252	15
α-helix	256-268	13
α-helix	273-283	11
α-helix	290-293	4
β-strand	294-297	4	2
α-helix	300-302	3
α-helix	305-310	6
β-strand	311-312	2	2
α-helix	313-315	3
α-helix	320-322	3
β-strand	324-330	7	2
β-strand	335-339	5	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymerase cofactor VP35	A, B	protein	129	Ebola virus	Q05127 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4IBD_1 Polymerase cofactor VP35 (chains A, B)
GHMGKPDISAKDLRNIMYDHLPGFGTAFHQLVQVICKLGKDSNSLDIIHAEFQASLAEGD
SPQCALIQITKRVPIFQDAAPPVIHIRSRGDIPRACQKSLRPVPPSPKIDRGWVCVFQLQ
DGKTLGLKI

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
1DL	5-[(2R)-3-benzoyl-2-(4-bromothiophen-2-yl)-4-hydroxy-5-oxo-2,5-dihydro-1H-pyrro…	C23 H16 Br N O5 S	2

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

Primary citation

In Silico Derived Small Molecules Bind the Filovirus VP35 Protein and Inhibit Its Polymerase Cofactor Activity. Brown, C.S., Lee, M.S., Leung, D.W. et al. J Mol Biol (2014) 426:2045-2058. DOI 10.1016/j.jmb.2014.01.010 · PubMed

Other PDB entries of the same protein (UniProt Q05127 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FKE 1.4 Å, Structure of the Ebola VP35 Interferon Inhibitory Domain
4IBG 1.41 Å, Ebola virus VP35 bound to small molecule
4IBI 1.47 Å, Ebola virus VP35 bound to small molecule
4IBJ 1.54 Å, Ebola virus VP35 bound to small molecule
3L29 1.7 Å, Crystal Structure of Zaire Ebola VP35 interferon inhibitory domain K319A/R322A mutant
4IBC 1.75 Å, Ebola virus VP35 bound to small molecule
4IBB 1.75 Å, Ebola virus VP35 bound to small molecule
4IBK 1.85 Å, Ebola virus VP35 bound to small molecule
4IJE 1.9 Å, Crystal structure of the Zaire ebolavirus VP35 interferon inhibitory domain…
3L27 1.95 Å, Crystal structure of Zaire Ebola VP35 interferon inhibitory domain R312A mutant
4IBE 1.95 Å, Ebola virus VP35 bound to small molecule
5BPV 1.95 Å, Crystal Structure of Zaire ebolavirus VP35 RNA binding domain mutant I278A

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