| Models |
The homology models of GPCRS were produced using rhodopsin crystal structure in the inactive conformation (1f88.pdb) as a template by residues substitution and side chain rotamer optimization to remove the major hindrances. To model the active conformation of rhodopsin its helix 6 was slightly rotated, to satisfy the experimental constraints, obtained by studies of spin-labeled and cross-linked rhodopsin. The loops were modeled from the rhodopsin template with a few inserted residues in the arbitrary conformations.
To remove the remaining hindrances the structure refinement was done by distance geomentry calculation using DIANA program, starting form the homology models of active and inactive conformations of the corresponding GPCRs, constrained by CB-CB distances between neighboring residues with 1 A deviations.
The ligand conformations were derived from their crystal structures or previously developed pharmacophore models. The QUANTA module DOCK was used for ligand docking.
Abbreviations: I – inactive conformation, A –active conformation, D – refined model by DIANA calculation.
|
|
Model Title |
Model Description |
Download |
Text |
|
1F88
|
Rhodopsin crystal structure (template, inactive form)
|
Download
|
Text
|
|
LSHR_RAT_ID
|
LH/hGH receptor (residues 335-622), inactive state
|
Download
|
Text
|
|
MC1R_HUMAN_ID_ASIP
|
MC1 melanocortin receptor (residues 35-317) with ASIP(93-132), inactive state
|
Download
|
Text
|
|
MC2R_HUMAN_AD_ACTH
|
ACTH receptor (residues 12-295) with ACTH(1-24), active state
|
Download
|
Text
|
|
MC4R_HUMAN_AD_AMSH
|
MC4 melanocortin receptor (residues 28-321) with alpha-MSH, active state
|
Download
|
Text
|
|
MC4R_HUMAN_AD_MB243
|
MC4 melanocortin receptor (residues 28-321) with MB243, active state
|
Download
|
Text
|
|
MC4R_HUMAN_AD_NDPMSH
|
MC4 melanocortin receptor (residues 28-321) with NDP-MSH, active state
|
Download
|
Text
|
|
MC4R_HUMAN_AD_THIQ
|
MC4 melanocortin receptor (residues 28-321) with THIQ, active state
|
Download
|
Text
|
|
MC4R_HUMAN_ID_AGRP
|
MC4 melanocortin receptor (residues 40-321) with AGRP(87-132), inactive state
|
Download
|
Text
|
|
MC4R_HUMAN_ID_ASIP
|
MC4 melanocortin receptor (residues 40-321) with ASIP(93-132), inactive state
|
Download
|
Text
|
|
NK1R_HUMAN_ID
|
NK1 receptor (residues 1-326), inactive state
|
Download
|
Text
|
|
NK2R_HUMAN_ID
|
NK2 receptor (residues 2-328), inactive state
|
Download
|
Text
|
|
NK3R_HUMAN_ID
|
NK3 receptor (residues 78-377), inactive state
|
Download
|
Text
|
|
OPRD_HUMAN_AD_JOM13
|
delta-opioid receptor (residues 45-336) with JOM13, active state
|
Download
|
Text
|
|
OPRK_HUMAN_AD_pep10
|
kappa-opioid receptor (residues 55-348) with pentapeptide 10, Tyr-c[DCys-Phe-Phe-DCys]NH2 (SS), active state
|
Download
|
Text
|
|
OPRM_RAT_AD_JOM6
|
mu-opioid receptor (residues 64-354) with JOM6, active state
|
Download
|
Text
|
|
OPRM_RAT_ID_BNI
|
mu-opioid receptor (residues 64-354) with nor-BNI, inactive state
|
Download
|
Text
|
|
OPRX_HUMAN_AD
|
nociceptin receptor (residues 47-337), active state
|
Download
|
Text
|
|
OPSD_BOVIN_AD
|
Bovine rhodopsin, active model (residues 1-326) with all-trans retinal, active state
|
Download
|
Text
|
Database links
|
|
|
Protein Data Bank (PDB)
, An archive of experimentally determined 3D-structures of biological macromolecule
|
|
|
SWISS-PROT and TrEMBL
, protein knowledgebase
|
|
|
SCOP
, Structural Classification of Proteins
|
|
|
CATH
, Hierarchical classification of protein structural relationships
|
|
|
FSSP
, Families of structurally similar proteins
|
|
|
PFAM
, Database of multiple sequence alignments
|
|
|
GPCRDB
, Database of G-protein coupled proteins
|
|
|
GPCRDBsup
, Supplement to GPCRDB
|
|
|
ModBase
, Database of 3D protein models
|
|
|
TRAMALDOM
, Our database of transmembrane alpha-helical domains with known structure
|
|
|
Orientations of Proteins in Membranes (OPM) database
, Our database that displays the tilt angles, hydrophobic thicknesses, delta G transfer, and other characteristics of transmembrane and periperal membrane proteins
|
Server links
|
|
|
BLAST
, Sequence alignment tools
|
|
|
3D-pssm
, Fold recognition server
|
|
|
PSIPRED
, A protein structure prediction server
|
|
|
PHDsec
, PredictProtein server at EMBL
|
|
|
Prediction Center
, Protein Structure Prediction Center
|
|
|
SWISS-MODEL
, Protein structure homology-modeling server
|
|
|
TMpred
, Prediction of Transmembrane Regions and Orientation
|
|
|
