4DKL

Crystal structure of the mu-opioid receptor bound to a morphinan antagonist

Structural Biology Knowledgebase: 4DKL SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.233

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DKL

Classification: SIGNALING PROTEIN / ANTAGONIST

Total Structure Weight: 55762.12

Macromolecule Entities
Molecule Chains Length Organism Details
Mu-type opioid receptor, lysozyme chimera A 464 Mus musculus Enterobacteria phage t4 sensu lato EC#: 3.2.1.17 IUBMB
Fragment: SEE REMARK 999
Mutation: D1020N, C1054T, C1097A
Gene Name(s): E Oprm1 Mor Oprm

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: G Protein-Coupled Receptors (GPCRs)

Protein Name: μ-opioid receptor bound to a morphinan antagonist


Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1PE
Query on 1PE

A PENTAETHYLENE GLYCOL
PEG400 (Synonym)
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
BF0
Query on BF0

A methyl 4-{[(5beta,6alpha)-17-(cyclopropylmethyl)- 3,14-dihydroxy-4,5-epoxymorphinan-6-yl]amino}- 4-oxobutanoate
beta-funaltrexamine, bound form (Synonym)
C25 H32 N2 O6
PGIBGSVRAVGQMY-OIUZVZFJSA-N
Ligand Explorer
 
JSmol
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
JSmol
CLR
Query on CLR

A CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Ligand Explorer
 
JSmol
MPG
Query on MPG

A [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
C21 H40 O4
JPJYKWFFJCWMPK-GDCKJWNLSA-N
Ligand Explorer
 
JSmol
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.275
  • R-Value Work: 0.233
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.88 α = 90.00
b = 174.73 β = 107.84
c = 68.35 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-03
  • Released Date: 2012-03-21
  • Deposition author(s): Manglik, A., Kruse, A.C., Kobilka, T.S., Thian, F.S., Mathiesen, J.M., Sunahara, R.K., Pardo, L., Weis, W.I., Kobilka, B.K., Granier, S.

Revision History

  • 2012-05-16
    Type: Citation | Details: Citation update