biology

Protein Data Bank (file format)

Protein Data Bank (file format) is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Protein Data Bank (file format) rather than just read about it. In short: The Protein Data Bank (PDB) file format is a textual file format describing the three-dimensional structures of molecules held in the Protein Data Bank, now succeeded by the mmCIF format. The PDB format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, secondary structure assignments, as well as atomic connectivity.

Key takeaways

Protein Data Bank (file format) belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Protein Data Bank (file format) to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Protein Data Bank (file format) from memory before moving on to harder problems.

Reference excerpt

The Protein Data Bank (PDB) file format is a textual file format describing the three-dimensional structures of molecules held in the Protein Data Bank, now succeeded by the mmCIF format. The PDB format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, secondary structure assignments, as well as atomic connectivity. In addition experimental metadata are stored. The PDB format is the legacy file format for the Protein Data Bank which has kept data on biological macromolecules in the newer PDBx/mmCIF file format since 2014.

History The PDB file format was invented in 1972 as a human-readable file that would allow researchers to exchange the atomic coordinates in a given protein through a database system. Its fixed-column width format is limited to 80 or 140 columns, which was based on the width of the computer punch cards that were previously used to exchange the coordinates. Through the years the file format has undergone many changes and revisions. The final update to the PDB file format was in November 2012 with version 3.30.

Example A typical PDB file describing a protein consists of hundreds to thousands of lines like the following (taken from a file describing the structure of a synthetic collagen-like peptide):

HEADER EXTRACELLULAR MATRIX 22-JAN-98 1A3I TITLE X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE TITLE 2 PEPTIDE WITH THE REPEATING SEQUENCE (PRO-PRO-GLY) ... EXPDTA X-RAY DIFFRACTION AUTHOR R.Z.KRAMER,L.VITAGLIANO,J.BELLA,R.BERISIO,L.MAZZARELLA, AUTHOR 2 B.BRODSKY,A.ZAGARI,H.M.BERMAN ... REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 ... SEQRES 1 A 9 PRO PRO GLY PRO PRO GLY PRO PRO GLY SEQRES 1 B 6 PRO PRO GLY PRO PRO GLY SEQRES 1 C 6 PRO PRO GLY PRO PRO GLY ... ATOM 1 N PRO A 1 8.316 21.206 21.530 1.00 17.44 N ATOM 2 CA PRO A 1 7.608 20.729 20.336 1.00 17.44 C ATOM 3 C PRO A 1 8.487 20.707 19.092 1.00 17.44 C ATOM 4 O PRO A 1 9.466 21.457 19.005 1.00 17.44 O ATOM 5 CB PRO A 1 6.460 21.723 20.211 1.00 22.26 C ... HETATM 130 C ACY 401 3.682 22.541 11.236 1.00 21.19 C HETATM 131 O ACY 401 2.807 23.097 10.553 1.00 21.19 O HETATM 132 OXT ACY 401 4.306 23.101 12.291 1.00 21.19 O ...

HEADER, TITLE and AUTHOR records provide information about the researchers who defined the structure; numerous other types of records are available to provide other types of information. REMARK records can contain free-form annotation, but they also accommodate standardized information; for example, the REMARK 350 BIOMT records describe how to compute the coordinates of the experimentally observed multimer from those of the explicitly specified ones of a single repeating unit. SEQRES records give the sequences of the three peptide chains (named A, B and C), which are very short in this example but usually span multiple lines. ATOM records describe the coordinates of the atoms that are part of the protein. For example, the first ATOM line above describes the alpha-N atom of the first residue of peptide chain A, which is a proline residue; the first three floating point numbers are its x, y and z coordinates and are in units of Ångströms. The next three columns are the occupancy, temperature factor, and the element name, respectively. HETATM records describe coordinates of hetero-atoms, that is those atoms which are not part of the protein molecule.

Molecular visualization software capable of displaying PDB files

3d Animation software capable of displaying PDB files

See also Chemical file format ScientificPython — provides an interface for Python Software for molecular mechanics modeling

References

External links PDB Format Guide This is the current version (3.3) of the PDB format specification. PDBML A more recent, alternative XML-based file format for molecular coordinates. The RCSB Protein Data Bank Protein Data Bank in Europe The Molecular Modeling DataBase (MMDB) from NCBI The wwPDB remediation Project from wwPDB MakeMultimer An online tool for expanding BIOMT records in PDB files Molecules iPad/iPhone App to display PDB files Python Macromolecular Library (mmLib) — a Python library capable of reading and writing PDB file formats

Worked examples

Example 1 — a first encounter with Protein Data Bank (file format)

Start with the simplest possible case. Write down what Protein Data Bank (file format) claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Protein Data Bank (file format) before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Protein Data Bank (file format) ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Protein Data Bank (file format)

In research: Protein Data Bank (file format) appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Protein Data Bank (file format) in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Protein Data Bank (file format) is common in secondary-school and first-year university syllabi. It links to neighbouring topics Biological sequence format, Chemical file formats, Computational chemistry, so understanding it makes those chapters shorter.
In everyday life: Look for Protein Data Bank (file format) outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study Protein Data Bank (file format) in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Protein Data Bank (file format) means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Protein Data Bank (file format) out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Protein Data Bank (file format) in simple terms?

Why does Protein Data Bank (file format) matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Protein Data Bank (file format)?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Protein Data Bank (file format).