SCHOOL OF PHARMACY

LAB REPORT 2

RETRIEVING SEQUENCE FROM

PROTEIN DATA BANK

BIOINFORMATICS
(PBI2020IP)
NAME STUDENT ID
RABIATUL ADAWIYAH BINTI 012020091691
HASBULLAH

PROGRAMME:
BACHELOR OF PHARMACEUTICAL
TECHNOLOGY (BPHT)

LECTURER :
AP DR SANTOSH FATTEPUR AND
DR ALICIA NG

DATE OF SUBMISSION:
2nd DECEMBER 2020
Practical 2: Retrieving sequence from Protein Data Bank

The Protein Data Bank (PDB) is a database for the 3-D structural data of large biological
molecules, such as proteins and nucleic acids. These are the molecules of life that are found
in all organisms including bacteria, yeast, plants, flies, other animals, and humans. The
Worldwide PDB (wwPDB) organization manages the PDB archive and ensures that the PDB
is freely and publicly available to the global community.

Introduction:

All information in PDB is available to the public. There are databases that contain information
derived from PDB. For example, Structural Classification of Proteins (SCOP) that bunches
different protein structures, HSSP (Homology-Derived Secondary Structure of Proteins) for
3D- structure, and 1D- sequence of the protein, CATH for protein structure classification
concurring to their evolution, and others. PDB permits searching for data regarding the
structure, sequence, function, visualize, download, and to evaluate atoms. Scientists have
decided the nuclear structures of thousands of the biomolecular components of cells. These
structures permit us to get to know cell biology at the atomic level. The secrets of protein
synthesis have been uncovered, beginning with the structure of DNA half a century prior,
uncovering the nuclear premise of genetic data, to the recent structures of working ribosomes,
caught within the act of translating this data into new proteins. The chemicals of glycolysis,
citric corrosive cycle, and electron transport have all been considered and their structures
have been decided. Three-dimensional (3D) structures are known for differing proteins of
sense, signaling, transport, control, and defense. These structures answer many important
natural questions, conjointly permit researchers to pose numerous new ones. Structural
bioinformatics is an area of bioinformatics centered on the structure, development, and
interaction of biological macromolecules in three-dimensional space. Structural bioinformatics
procedures play a vital part in drug discovery and can be utilized at each stage of the medicate
plan process, where they can be utilized to complement, and some of the time replace more
expensive test methods. For case, the protein structure prediction program gives choices to
X-ray crystallography and NMR methods, whereas virtual screening and atomic flow
recreations can complement High-Throughput Screening (HTS). The utilize of computational
methods in drug disclosure and plan is regularly referred to as Computer-Aided Medicate Plan
(CADD). In this section, we'll examine the uses of structural bioinformatics as a portion of
CADD, particularly within the context of non-synonymous SNP analysis. Mutations have been
related to drug resistance in various illnesses such as influenza, tuberculosis, HIV, and cancer.
Similarly, mutations can be connected to drug affectability in patients. This opens the door to
personalized solutions, where information on drug safety and drug-sensitive SNPs permit
medications to be custom-made to individual patients. Understanding structural changes
caused by non-synonymous SNPs will empower the design of novel drugs to target these
mutations and, hence, be key in progressing personalized medicine.

Aim:

To retrieve structural information of TWO (2) protein (PDB ID: 3V99 and 2JFF) from PDB.
Procedure:

1. Analyze the structure summary based on the followings: (20%, each protein 10%)

a) Name 1%
b) Classification 1%
c) Organism 1%
d) Method of experimental data snapshot 1%
e) Resolution 1%
f) Experimental data snapshot 1%
g) No. of chains 1%
h) Sequence length 1%
i) UniprotKB ID 1%
j) Examples of small ligands 1%

2. View the 3D structure of protein using [3D view] tab tools as follow: (48%, each protein 24
marks)

a) Whole structure (click on Toggle Expanded Viewport) then print screen 3%

b) Select any one letter code of amino acid (on top) then print screen 3%
c) Show only ligand molecule 3%
d) Show only protein molecule 3%
e) Show ligand and protein complex 3%
f) Try on how to use the button for screenshotting the complex (ligand and protein)
3%
g) Change the background to black color and print screen 3%
h) Change the background to white color and choose clipping at 80 then print screen 3%

3. Display FASTA sequence of the protein by click on [Display Files] and [FASTA sequence].
(2%, each protein 1%)

4. Paste all your print screens on MS word.

PDB ID: 3V99

1.
a) Name

S663D Stable-5-LOX in complex with Arachidonic Acid

b) Classification

OXIDOREDUCTASE

c) Organism

Homo sapiens

d) Method of experimental data snapshot

X-RAY DIFFRACTION

e) Resolution

2.25A

f) Experimental data snapshot

How online games helps in improving mental health

g) No. of chains

Unique protein chains: 1

h) Sequence length

691

i) UniprotKB ID

P09917
 j) Examples of small ligands

2.
a) Whole structure (click on Toggle Expanded Viewport) then print screen
b) Select any one letter code of amino acid (on top) then print screen
c) Show only ligand molecule

d) Show only protein molecule

e) Show ligand and protein complex

f) Try on how to use the button for screenshotting the complex (ligand and protein)
g) Change the background to black color and print screen

h) Change the background to white color and choose clipping at 80 then print screen
3. Display FASTA sequence of the protein by click on [Display Files] and [FASTA
sequence].

>3V99_1|Chains A,B|Arachidonate 5-lipoxygenase|Homo sapiens (9606)

MGSSHHHHHHSSGLVPRGSHMPSYTVTVATGSQEHAGTDDYIYLSLVGSAGCSEKHLLDK
GSFERGAVDSYDVTVDEELGEIQLVRIEKRKYGSNDDWYLKYITLKTPHGDYIEFPCYRWIT
GDVEVVLRDGRAKLARDDQIHILKQHRRKELETRQKQYRWMEWNPGFPLSIDAKCHKDLP
RDIQFDSEKGVDFVLNYSKAMENLFINRFMHMFQSSWNDFADFEKIFVKISNTISERVMNH
WQEDLMFGYQFLNGANPVLIRRCTELPEKLPVTTEMVECSLERQLSLEQEVQQGNIFIVDF
ELLDGIDANKTDPCTLQFLAAPICLLYKNLANKIVPIAIQLNQIPGDENPIFLPSDAKYDWLLAK
IWVRSSDFHVHQTITHLLRTHLVSEVFGIAMYRQLPAVHPIFKLLVAHVRFTIAINTKAREQLI
CECGLFDKANATGGGGHVQMVQRAMKDLTYASLCFPEAIKARGMESKEDIPYYFYRDDGL
LVWEAIRTFTAEVVDIYYEGDQVVEEDPELQDFVNDVYVYGMRGRKSSGFPKSVKSREQL
SEYLTVVIFTASAQHAAVNFGQYDWASWIPNAPPTMRAPPPTAKGVVTIEQIVDTLPDRGR
SCWHLGAVWALSQFQENELFLGMYPEEHFIEKPVKEAMARFRKNLEAIVSVIAERNENLQL
PYYYLDPDRIPNSVAI
PDB ID: 2JFF

1.

a) Name

Crystal structure of MurD ligase in complex with D-Glu containing sulfonamide inhibitor

b) Classification

LIGASE

c) Organism

Escherichia coli

d) Method of experimental data snapshot

X-RAY DIFFRACTION

e) Resolution

1.89 A

f) Experimental data snapshot

g) No. of chains

Unique protein chains: 1

h) Sequence length

445

i) UniprotKB ID

P14900
 j) Examples of small ligands

2.
a) Whole structure (click on Toggle Expanded Viewport) then print screen
b) Select any one letter code of amino acid (on top) then print screen
c) Show only ligand molecule

d) Show only protein molecule

e) Show ligand and protein complex

f) Try on how to use the button for screenshotting the complex (ligand and protein)
g) Change the background to black color and print screen

h) Change the background to white color and choose clipping at 80 then print screen
3. Display FASTA sequence of the protein by click on [Display Files] and [FASTA sequence].

>2JFF_1|Chain A|UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE
LIGASE|ESCHERICHIA COLI (562)
MADYQGKNVVIIGLGLTGLSCVDFFLARGVTPRVMDTRMTPPGLDKLPEAVERHTGSLNDE
WLMAADLIVASPGIALAHPSLSAAADAGIEIVGDIELFCREAQAPIVAITGSNGKSTVTTLVGE
MAKAAGVNVGVGGNIGLPALMLLDDECELYVLELSSFQLETTSSLQAVAATILNVTEDHMD
RYPFGLQQYRAAKLRIYENAKVCVVNADDALTMPIRGADERCVSFGVNMGDYHLNHQQGE
TWLRVKGEKVLNVKEMKLSGQHNYTNALAALALADAAGLPRASSLKALTTFTGLPHRFEVV
LEHNGVRWINDSKATNVGSTEAALNGLHVDGTLHLLLGGDGKSADFSPLARYLNGDNVRL
YCFGRDGAQLAALRPEVAEQTETMEQAMRLLAPRVQPGDMVLLSPACASLDQFKNFEQR
GNEFARLAKELGSHHHHHH

Conclusion

The Protein Data Bank (PDB) presently contains more than 120,000 three-dimensional (3D)
structures of biological macromolecules. To permit a translation of how PDB information
relates to other freely accessible explanations, they created a novel information integration
platform that maps 3D basic data over different datasets. This integration bridges from the
human genome over protein sequence to 3D structure space. they created novel computer
program solutions for information administration and visualization, whereas incorporating new
libraries for web-based visualization utilizing SVG illustrations.