StrucPTM Database
Structurally validated PTM residues and their conformational variation
StrucPTM database provides integrated information on post-translationally modified (PTM) residues by examining residue names and validating their atom composition in PDB structures. Using SIFTS (Structure Integration with Function, Taxonomy and Sequences), we first assemble sets of related PDB chains; we then perform sequence alignment among those chains to identify highly similar or identical sequences. This allows direct comparison of structures that share the same sequence but differ in PTM states, thereby enabling the analysis of structural alterations induced by PTMs.
PTM-driven conformational change: insulin receptor kinase
Phosphorylation can reorganize the three-dimensional structure of a signaling protein in a highly coordinated manner. The movie on the right visualizes an interpolation between an inactive insulin receptor kinase structure (
1IRK) and an active, phosphorylated state (1IR3), highlighting how activation-loop phosphorylation is coupled to large rigid-body motions.Morph between inactive (1IRK) and active (1IR3) insulin receptor kinase structures. The trajectory illustrates how phosphorylation of the activation loop can propagate through the kinase core and reorganize the overall conformation. (Daily MD, Gray JJ (2009) Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins. PLoS Comput Biol 5(2): e1000293. https://doi.org/10.1371/journal.pcbi.1000293)
Why PTMs matter
In StrucPTM, each PTM site is annotated at residue level on deposited structures. This makes it possible to compare "OFF-like" and "ON-like" conformations along with their PTM status. Src kinase is a classic example where phosphorylation at a regulatory tyrosine and changes in activation-loop conformation together control signaling output. Comparing 1Y57 (an ON-like active conformation) and 2SRC (an OFF-like autoinhibited, phosphorylated conformation) illustrates how phosphorylation at the regulatory tyrosine can switch Src from an ON to an OFF state.
Src kinase active-like conformation without regulatory phosphorylation (1Y57)
This structure adopts an open activation loop and represents an "ON-like" active conformation of Src kinase. In the current StrucPTM data, no inhibitory phosphorylation at the regulatory tail is annotated for this PDB ID. By placing 1Y57 side-by-side with 2SRC, users can examine how loss of regulatory phosphorylation correlates with activation of the kinase domain.
Src kinase autoinhibited conformation with regulatory phosphorylation (2SRC)
This structure contains a phosphorylated regulatory tyrosine (for example, Tyr527 in chain A), annotated as a PTM residue. The overall fold represents an autoinhibited, "OFF-like" conformation in which intramolecular interactions involving the phosphorylated tail keep the kinase domain restrained. StrucPTM highlights such phosphorylated residues directly on the structure viewer, making it easy to relate PTM status to conformational state.
Statistics
All statistics below summarize PTM sites that have passed the StrucPTM processing and validation pipeline. The underlying structural data originate from Protein Data Bank (PDB) mmCIF entries. In the current build, StrucPTM contains 0 PTM sites that satisfied our filtering criteria, distributed across – unique mmCIF structures with at least one PTM annotation. The PDB snapshot used for this build corresponds to entries available as of
unknown.PTM Type
No data
Residue Type
No data
Organism
No data
BIS Lab
About
Bioinformatics and Intelligent Systems Lab (BIS Lab)
Department of Computer Science, Hanyang University
Department of Computer Science, Hanyang University
Address
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Wangsimni-ro, Seongdong-gu
Seoul, Republic of Korea
Wangsimni-ro, Seongdong-gu
Seoul, Republic of Korea
Contact info
prix@hanyang.ac.kr