!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 22.0.3 is available.
You should consider upgrading via the '/usr/bin/python3 -m pip install --upgrade pip' command.

Задание 1)

import nglview as nv # Импорт всего нужного
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": "diclofenac" # Ключевое слово
    }
}

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

resolution_clause = {
    "type": "terminal",
    "service": "text",
    "parameters": {
        "value": 2.3, # Разрешение 2.3 ангстрем и выше
        "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,               # Больше 0 лигандов,
        "operator": "greater"     # то есть не меньше 1
    }
}

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": "2000-01-01", # Дата с 2000-01-01 
            "to": "2005-01-01",   # по 2005-01-01
        },
        "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) # Отправляем запрос

search # Проверяем что все хорошо

<Response [200]>

search_result = search.json()              # Распаковываем результат в словарь
best_hit = search_result["result_set"][0]  # Выделяем лучшую находку

best_hit

{'identifier': '1NR6',
 'score': 0.9998151270802235,
 'services': [{'service_type': 'full_text',
   'nodes': [{'node_id': 28491,
     'original_score': 16.152864456176758,
     'norm_score': 0.9992605083208939}]},
  {'service_type': 'text',
   'nodes': [{'node_id': 5681, 'original_score': 1.0, 'norm_score': 1.0},
    {'node_id': 10901, 'original_score': 1.0, 'norm_score': 1.0},
    {'node_id': 2261, 'original_score': 1.0, 'norm_score': 1.0}]}]}

Тем самым мы имеем то что необходимый нам PDB ID - 1NR6

Задание 2)

Структуру противовоспалительного препарата диклофенака, связанного в активном центре микросомального цитохрома P450 кролика 2C5/3LVdH, определяли с помощью рентгеноструктурного анализа с разрешением 2,1 Å. P450 2C5/3LVdH и родственный фермент 2C5dH катализируют 4'-гидроксилирование диклофенака с кажущимися значениями K(m) 80 и 57 мкМ и значениями k(cat) 13 и 16 мин(-1) соответственно. Спектрально определенные константы связывания аналогичны значениям K(m). Структура указывает на то, что пи-электронная система дихлорфенильного фрагмента обращена к гему Fe с 3'- и 4'-углеродами, расположенными на расстоянии 4,4 и 4,7 Å от Fe соответственно. Карбоксильная часть субстрата связана водородной связью с группой вод, которые также связаны водородной связью с боковыми цепями N204, K241, S289 и D290, а также с основной цепью белка. Близость карбоксилата диклофенака к боковой цепи D290 вместе с повышенной аффинностью связывания при более низком pH предполагает, что диклофенак протонируется при связывании с ферментом. Структура демонстрирует конформационные изменения, указывающие на адаптивную подгонку к субстрату, отражающую как гидратацию, так и размер субстрата. Эти результаты показывают, как структурно разнообразные субстраты распознаются ферментами P450, метаболизирующими лекарственные средства.

Задание 3)

view = nv.show_pdbid('1NR6') 
view

from ipywidgets import interact, fixed

my_examples = {
    'Example 1': {
        'description': '''
Белок в виде cartoon, покраска от N к C концу
Боковые радикалы покрашены в светло-серый, показаны линиями
Боковые радикалы заряженных аминокислот показаны в стержневой модели
Лиганды показаны в шаростержневой модели, покрашены по элементам, углерод покрашен в любой цвет, кроме стандартного
''',
        'representations': [
            {
                'type': 'cartoon',                      
                'params': {
                    'sele': 'protein',              
                    'color': 'residueindex'
                 }
            },
            {
                'type': 'line',
                'params': {
                    'sele': 'sidechain',                 
                    'color': 'lightgray'  
                 }
            },
            {
                'type': 'licorice',                      
                'params': {
                    'sele': 'charged',                
                    'color': 'lightgray'  
                 }
            },
            {
                'type': 'ball+stick',                      
                'params': {
                    'sele': 'ligand',               
                    'color': 'element'  
                 }
            },
            {
                'type': 'ball+stick',                      
                'params': {
                    'sele': 'ligand and _C',            
                    'color': 'turquoise', 
                 }
            },
        ],
    },
    'Example 2': {
        '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': 'sidechain',                 
                    'color': 'hydrophobicity'  
                 }
            },
            {
                'type': 'line',                      
                'params': {
                    'sele': 'ligand C',                
                    'color': 'element'  
                 }
            },
            {
                'type': 'spacefill',                      
                'params': {
                    'sele': 'water',               
                    'color': 'element'  
                 }
            },
            {
                'type': 'spacefill',                      
                'params': {
                    'sele': 'ion',            
                    'color': 'element', 
                 }
            },
        ],
    },
    'Example 3': {
        'description': '''
Остов белка в шаростержневой модели, покрашен по элементам
Боковые радикалы в стержневой модели, покрашены по элементам
Углероды остатков с 30 по 70-й покрашены в светло-голубой
Лиганды показаны в виде линий, покрашены в любой оттенок оранжевого
''',
        'representations': [
            {
                'type': 'ball+stick',                      
                'params': {
                    'sele': 'backbone',               
                    'color': 'element'  
                 }
            },
            {
                'type': 'licorice',                      
                'params': {
                    'sele': 'sidechain',                     
                    'color': 'element'  
                 }
            },
            {
                'type': 'ball+stick',                      
                'params': {
                    'sele': 'protein and :A and 1030-1070 and _C',
                    'color': 'lightblue'  
                 }
            },
            {
                'type': 'line',
                'params': {
                    'sele': 'ligand',                     
                    'color': 'orange'  
                 }
            },
        ],
    },
}

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("1NR6", default_representation=False)
interact(show_examples, view=fixed(view), example_name=list(my_examples.keys()))
view