5C1M

Crystal structure of active mu-opioid receptor bound to the agonist BU72


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.185

Literature

Macromolecules
Sequence Display for 5C1M

Classification: Signaling Protein / antagonist

Total Structure Weight: 49585.21

Macromolecule Entities
Molecule Chains Length Organism Details
Mu-type opioid receptor A 296 Mus musculus Gene Name(s): Oprm1 Mor Oprm
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Nanobody 39 B 125 Lama glama

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 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
4VO
Query on 4VO

A (2S,3S,3aR,5aR,6R,11bR,11cS)-3a-methoxy-3,14- dimethyl-2-phenyl-2,3,3a,6,7,11c-hexahydro- 1H-6,11b-(epiminoethano)-3,5a-methanonaphtho[2,1- g]indol-10-ol
BU72 (Synonym)
C28 H32 N2 O2
RGJHUVJQGAAZLK-CLYKQLRXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CLR
Query on CLR

A CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OLC
Query on OLC

A (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol (Synonym)
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
P6G
Query on P6G

A HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400 (Synonym)
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
YCM
Query on YCM
A L-PEPTIDE LINKING C5 H10 N2 O3 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.185
  • Space Group: I 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 44.43 α = 90.00
b = 144.00 β = 90.00
c = 209.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-06-15
  • Released Date: 2015-08-05
  • Deposition author(s): Huang, W.J., Manglik, A., Venkatakrishnan, A.J., Laeremans, T., Feinberg, E.N., Sanborn, A.L., Kato, H.E., Livingston, K.E., Thorsen, T.S., Kling, R., Granier, S., Gmeiner, P., Husbands, S.M., Traynor, J.R., Weis, W.I., Steyaert, J., Dror, R.O., Kobilka, B.K.

Revision History

  • Version 1_0: 2015-08-05

    Type: Initial release

  • Version 1_1: 2015-08-19

    Type: Database references

  • Version 1_2: 2015-08-26

    Type: Data collection

  • Version 1_3: 2015-09-02

    Type: Database references

  • Version 1_4: 2017-09-06

    Type: Author supporting evidence, Database references, Derived calculations