4DN0

PelD 156-455 from Pseudomonas aeruginosa PA14 in complex with c-di-GMP

Structural Biology Knowledgebase: 4DN0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.201

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DN0

Classification: Nucleotide-binding Protein

Total Structure Weight: 37583.17

Macromolecule Entities
Molecule Chains Length Organism Details
Putative uncharacterized protein pelD A 321 Pseudomonas aeruginosa Fragment: Soluble fragment
Gene Name(s): pelD PA14_24510

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
C2E
Query on C2E

A 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)- 3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro- 2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine- 2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin- 6-one)
c-di-GMP, Cyclic diguanosine monophosphate (Synonym)
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
C2E N/A in BindingDB
Kd: 1900 nM  BindingMOAD
Kd: 1900 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.201
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 41.78 α = 90.00
b = 82.04 β = 90.00
c = 91.81 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-08
  • Released Date: 2012-05-23
  • Deposition author(s): Whitney, J.C., Colvin, K.M., Marmont, L.S., Robinson, H., Parsek, M.R., Howell, P.L.

Revision History

  • 2012-07-25
    Type: Citation | Details: Citation update
  • 2012-05-30
    Type: Citation | Details: Citation update