Guide to Understanding PDB Data: Computed Structure Models

03/27 

The crystallographic structure of the inactive conformation (left, PDB ID 2src) reveals the atomic details of the recognition of phosphotyrosine (red and pink spacefill) by the SH2 domain, but is missing the N-terminal tail. The crystallographic structure is colored to highlight the functional domains - Protein kinase (orange), SH2 domain in light blue, and SH3 domain in dark blue.
The Computed Structure Model of human Src oncogene protein predicted by AlphaFold2 (RCSB.org assigned ID AF_AFP12931F1, right), is colored by confidence level (pLDDT scores). The model includes a compact folded structure with good confidence that corresponds to the inactive conformation of the protein, but with an unphosphorylated form of the tyrosine (pink). The model includes a long unstructured N-terminal tail with very low confidence.

The constantly-growing PDB is a reflection of the research that is happening in laboratories across the world and the evolving technologies that can be used to harness the power of these data.

PDB-101's Guide to Understanding PDB Data was created to help users navigate through the contents of the archive without having a detailed background in structural biology or computer science.

Guide topics cover biological assemblies, molecular graphics programs, R-value and R-free, and more. Articles are released to help explain new features as they are added to RCSB.org, such as the inclusion of of Computed Structure Models at RCSB.org

The CSM chapter provides an introduction to how these data are generated, and how to assess the trustworthiness of a predicted structure.

Topics in this article include:

• Introduction
• Protein Structure Prediction
• Generating Computed Structure Models
• Using Computed Structure Models
• Case Study: Computed Structure Model of the Src Oncoprotein

RCSB.org offers access to >1 million Computed Structure Models (CSMs) from AlphaFoldDB and RoseTTAFold (from ModelArchive).

Only experimentally-determined PDB structures are included in search results by default. Move the "Include CSM" from gray- to cyan-colored slider to activate.

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