!pip install nglview --user

/usr/lib/python3/dist-packages/secretstorage/dhcrypto.py:15: CryptographyDeprecationWarning: int_from_bytes is deprecated, use int.from_bytes instead
  from cryptography.utils import int_from_bytes
/usr/lib/python3/dist-packages/secretstorage/util.py:19: CryptographyDeprecationWarning: int_from_bytes is deprecated, use int.from_bytes instead
  from cryptography.utils import int_from_bytes
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WARNING: You are using pip version 21.0.1; however, version 22.1 is available.
You should consider upgrading via the '/usr/bin/python3 -m pip install --upgrade pip' command.

import nglview as nv 
import requests
import json

my_query = {
    "query": {
        "type": "group",
        "logical_operator": "and",
        "nodes": []
    },
    "return_type": "entry"
}

keyword_clause = {
    "type": "terminal",
    "service": "full_text", 
    "parameters": {
        "value": "serotonin" 
    }
}

my_query["query"]["nodes"].append(keyword_clause)

resolution_clause = {
    "type": "terminal",
    "service": "text",
    "parameters": {
        "value": 2.7, 
        "attribute": "rcsb_entry_info.resolution_combined",
        "operator": "less_or_equal"
    }
}

my_query["query"]["nodes"].append(resolution_clause)

has_ligand_clause = {
    "type": "terminal",
    "service": "text",
    "parameters": {
        "attribute": "rcsb_entry_info.nonpolymer_entity_count",
        "value": 0,               
        "operator": "greater"     
    }
}

my_query["query"]["nodes"].append(has_ligand_clause)

date_range_clause = {
    "type": "terminal",
    "service": "text",
    "parameters": {
        "attribute": "rcsb_accession_info.initial_release_date",
        "value": {
            "from": "2010-01-01", 
            "to": "2015-01-01",   
        },
        "operator": "range"
    }
}

my_query["query"]["nodes"].append(date_range_clause)

rcsb = 'https://search.rcsb.org/rcsbsearch/v1/query'
json_query = json.dumps(my_query)
search = requests.post(f'{rcsb}', data=json_query) 

search

<Response [200]>

search_result = search.json()              
best_hit = search_result["result_set"][0]

best_hit

{'identifier': '4IAR',
 'score': 0.99862133438031,
 'services': [{'service_type': 'full_text',
   'nodes': [{'node_id': 26531,
     'original_score': 10.5161771774292,
     'norm_score': 0.99448533752124}]},
  {'service_type': 'text',
   'nodes': [{'node_id': 2561, 'original_score': 1.0, 'norm_score': 1.0},
    {'node_id': 14643, 'original_score': 1.0, 'norm_score': 1.0},
    {'node_id': 149, 'original_score': 1.0, 'norm_score': 1.0}]}]}

from ipywidgets import interact, fixed

representations = [                                                          
  'ball+stick',      
  'backbone',        
  'cartoon',         
  'helixorient',    
  'hyperball',      
  'licorice',        
  'line',            
  'point',         
  'ribbon',         
  'rocket',          
  'rope',           
  'spacefill',      
  'surface',      
  'trace',           
  'tube'             ]

colors = [                                                                 
  'random',
  'uniform',
  'atomindex',      
  'residueindex',   
  'chainindex',     
  'sstruc',        
  'element',       
  'resname',      
  'bfactor',       
  'hydrophobicity', ]

my_examples = {         
    'view_5': {
        'description': '''
Белок в виде tube, покраска по типу вторичной структуры
Боковые радикалы в стержневой модели, покрашены по гидрофобности
Лиганды показаны линиями, покрашены по элементам
Вода и ионы показаны в виде Ван-дер-Ваальсовых сфер
''',
        'representations': [
            {
                'type': 'tube',                      
                'params': {
                    'sele': 'protein',              
                    'color': 'sstruc'
                 }
            },
            {
                'type': 'licorice',
                'params': {
                    'sele': 'sidechainAttached',                 
                    'color': 'hydrophobicity'  
                 }
            },
            {
                'type': 'line',                      
                'params': {
                    'sele': 'ligand',               
                    'color': 'element'  
                }
            },
            {
                'type': 'spacefill',
                'params': {
                    'sele': 'water and ion',
                    }
            },
    ],
},
     'view_6': {
        'description': '''
Белок в виде cartoon темно-серого цвета
Боковые радикалы в виде линий светло-серого цвета
Боковые радикалы полярных аминокислот в виде hyperball, покрашены по элементам
Лиганды в шаростержневой модели, покрашены по элементам, углероды покрашены в темно-синий
''',
    'representations': [
        {
            'type': 'cartoon',
            'params':
            {
                'sele': 'protein',
                'color': 'darkgrey'
            }
        },
        {
            'type': 'line',
            'params':
            {
               'sele': 'sidechainAttached',
                'color': 'lightgrey'
            }
        },
        {
            'type': 'hyperball',
            'params':
            {
                'sele': 'sidechainAttached and aromatic',
                'color': 'element'
            }
        },
        {
            'type': 'ball+stick',
            'params':
            {
                'sele': 'ligand and not _C',
                'color': 'element'

            }
        },
        {
            'type': 'ball+stick',
            'params':
            {
                'sele': 'ligand and _C',
                'color': 'darkblue'}
        },
    ],
},
    'view_7': {
        'description': '''
Белок в виде ribbon, покрашенной градиентом от N к C концу
Боковые радикалы в стержневой модели, покрашенные по элементам
Углероды гидрофобных аминокислот покрашены в светло-желтый
Углероды полярных заряженных аминокислот покрашены в светло-голубой
Лиганды не показаны никак
''',
        'representations': [  {"type":"ribbon",
                 "params":{"color":"atomindex",
                           "sele":"protein"}
                },
               
               {"type":"ball+stick",
                "params":{"color":"element",
                         "sele":"sidechainAttached"}
               },
               
               {"type":"ball+stick",
                "params":{"color":"#FFF700",
                         "sele":"_C and hydrophobic"}
                },
                {"type":"ball+stick",
                "params":{"color":"#40cfff",
                         "sele":"_C and charged"}
                },
                 
                {"type":"none",
                 "params":{"sele":"ligand"}}
         ]
    },
}

def show_examples(view, example_name):
    view.clear()
    example = my_examples[example_name]
    print(example['description'])
    view.set_representations(example['representations'])
    view.center()

view = nv.show_pdbid("4iar", default_representation=False)
interact(show_examples, view=fixed(view), example_name=list(my_examples.keys()))
view

Запись, найденная по идентификатору 4iar, содержит информацию о гормоне серотонине (5-гидрокситриптамин). Он регулирует широкий спектр физиологии человека через семейство рецепторов 5-НТ. Запись сообщает о кристаллических структурах рецептора, связанного с белком 5-HT1B G человека, связанного с агонистами противомигриновых препаратов эрготамином и дигидроэрготамином. Данные структуры обнаруживают сходные режимы связывания для этих лигандов. . По сравнению со структурой рецептора 5-HT2B, рецептор 5-HT1B демонстрирует смещение наружу на 3 ангстрема на внеклеточном конце спирали V, что приводит к более открытому расширенному карману, что объясняет селективность подтипа. Следовательно, структуры обеспечивают всеобъемлющую структурную основу для понимания взаимодействий рецептор-лиганд и разработки подтип-селективных серотонинергических d.