4IBD

Ebola virus VP35 bound to small molecule

Structural Biology Knowledgebase: 4IBD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.177

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4IBD

Classification: TRANSCRIPTION / TRANSCRIPTION inhibitor

Total Structure Weight: 29626.39

Macromolecule Entities
Molecule Chains Length Organism Details
Polymerase cofactor VP35 A, B 129 Zaire ebolavirus Fragment: unp residues 215-340
Gene Name(s): VP35

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1DL
Query on 1DL

A, B 5-[(2R)-3-benzoyl-2-(4-bromothiophen-2-yl)- 4-hydroxy-5-oxo-2,5-dihydro-1H-pyrrol-1-yl]- 2-methylbenzoic acid
C23 H16 Br N O5 S
YQDONULRFRLRSB-IBGZPJMESA-N
Ligand Explorer
 
JSmol
GOL
Query on GOL

A, B GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
MG
Query on MG

B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
1DL N/A in BindingDB
Kd: 214600 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.177
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 51.56 α = 90.00
b = 65.49 β = 90.00
c = 72.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-08
  • Released Date: 2014-03-19
  • Deposition author(s): Brown, C.S., Leung, D.W., Xu, W., Borek, D.M., Otwinowski, Z., Ramanan, P., Stubbs, A.J., Peterson, D.S., Binning, J.M., Amarasinghe, G.K.

Revision History

  • 2014-05-14
    Type: Citation | Details: Citation update