1. Updates

Weekly updates. StrucPTM is rebuilt on a weekly basis using the latest PDB mmCIF, SIFTS, and UniProt releases; DSSP-derived annotations are recomputed for each build.

2. Web interface usage

The StrucPTM web interface can be understood in four parts: search filters, search results, PDB selection for comparison, and comparison view.
  1. Search filters. In the Search tab, specify UniProt ID or PDB ID:Chain (e.g. 132L:A), then optionally refine by PTM type, assembly type, location, secondary structure, and RSA range.
  2. Search results. The results table lists curated PTM entries matching the filters. Each row shows identifiers and structural context.
  3. PDB selection for comparison. Clicking Compare opens a view where you can select homologous PDB chains (from the same UniProt) as comparison targets.
  4. Comparison view. Selected structures are shown in a 3D viewer. The PTM residue is highlighted with residue number and residue name, and the sequence alignment results are displayed below the viewer.

3. Atomic composition rules for PTM validation

For selected PTM types, StrucPTM validates each modified residue by checking that the atom set in the mmCIF file matches an expected canonical + added atoms pattern. The table below lists the atomic composition rules used in this release.
PTM TypeCanonical ResidueCanonical AtomsPTM Residue (PDB code)Added Atoms
AcetylationAlanine (ALA)N, CA, C, O, CBN-acetyl-alanine (AYA)OT, CT, CM
AcetylationLysine (LYS)N, CA, C, O, CB, CG, CD, CE, NZN6-acetyl-lysine (ALY)CH, CH3, OH
AcetylationSerine (SER)N, CA, C, O, CB, OGO-acetyl-serine (SAC)C2A, C1A, OAC
FormylationMethionine (MET)N, CA, C, O, CB, CG, SD, CEN-formyl-methionine (FME)O1, CN
Gamma-carboxyglutamic acidGlutamic acid (GLU)N, CA, C, O, CB, CG, CD, OE1, OE2carboxy-glutamic acid (CGU)OE21, OE22, OE11, CD2, OE12, CD1
HydroxylationLysine (LYS)N, CA, C, O, CB, CG, CD, CE, NZHydroxy-lysine (LYZ)OH
HydroxylationProline (PRO)N, CA, C, O, CB, CG, CD4-hydroxy-proline (HYP)OD1
MethylationArginine (ARG)N, CA, C, O, CB, CG, CD, NE, CZ, NH1, NH2Methyl-arginine (AGM)NE1, CE2
MethylationAsparagine (ASN)N, CA, C, O, CB, CG, OD1, ND2Methyl-asparagine (MEN)CE2
MethylationCysteine (CYS)N, CA, C, O, CB, SGS-methyl-cysteine (SMC)CS
MethylationCysteine (CYS)N, CA, C, O, CB, SGS-methyl-cysteine (CMT)C1
MethylationGlutamine (GLN)N, CA, C, O, CB, CG, CD, OE1, NE2Methyl-glutamine (MGN)CB1, CB2
MethylationGlutamic acid (GLU)N, CA, C, O, CB, CG, CD, OE1, OE2Methyl-glutamic acid (MEA)C1, CD2, CZ, CE2, CE1, CD1
MethylationHistidine (HIS)N, CA, C, O, CB, CG, ND1, CD2, CE1, NE2Methyl-histidine (HIC)CZ
MethylationHistidine (HIS)N, CA, C, O, CB, CG, ND1, CD2, CE1, NE2Methyl-histidine (MHS)CM
MethylationLysine (LYS)N, CA, C, O, CB, CG, CD, CE, NZN6-methyl-lysine (MLY)CH2, CH1
MethylationLysine (LYS)N, CA, C, O, CB, CG, CD, CE, NZN6,N6,N6-trimethyl-lysine (M3L)CM3, CM1, CM2
MethylationLysine (LYS)N, CA, C, O, CB, CG, CD, CE, NZMethyl-lysine (MLZ)CM
N6-carboxylysineLysine (LYS)N, CA, C, O, CB, CG, CD, CE, NZN6-carboxy-lysine (KCX)OQ2, OQ1, CX
NitrationTyrosine (TYR)N, CA, C, O, CB, CG, CD1, CD2, CE1, CE2, CZ, OH3-nitro-tyrosine (NIY)O2, NN, O1
OxidationCysteine (CYS)N, CA, C, O, CB, SGCysteine sulfenic acid (CSO)OD
OxidationMethionine (MET)N, CA, C, O, CB, CG, SD, CEMethionine sulfoxide (OMT)OD1, OD2
PhosphorylationSerine (SER)N, CA, C, O, CB, OGO-phospho-serine (SEP)O3P, P, O1P, O2P
PhosphorylationThreonine (THR)N, CA, C, O, CB, OG1, CG2O-phospho-threonine (TPO)O3P, P, O1P, O2P
PhosphorylationTyrosine (TYR)N, CA, C, O, CB, CG, CD1, CD2, CE1, CE2, CZ, OHO-phospho-tyrosine (PTR)O3P, P, O1P, O2P
Pyrrolidone carboxylic acidGlutamine (GLN)N, CA, C, O, CB, CG, CD, OE1, NE2Pyro-glutamate (PCA)OE
S-NitrosylationCysteine (CYS)N, CA, C, O, CB, SGS-nitroso-cysteine (SNC)OE, ND
SulfationTyrosine (TYR)N, CA, C, O, CB, CG, CD1, CD2, CE1, CE2, CZ, OHO-sulfo-tyrosine (TYS)O2, O3, S, O1
Canonical atoms correspond to the backbone and side-chain atoms of the unmodified residue. “Added atoms” represent additional atoms introduced by the PTM group and must be present for a residue to be considered a valid instance of that PTM.

4. API access

StrucPTM provides programmatic access via a REST API. Interactive API documentation (Swagger UI) is available at https://prix.hanyang.ac.kr/strucptm/api/docs.
The API base URL is https://prix.hanyang.ac.kr/strucptm/api. The primary endpoint is POST /search_ptm_data, which returns curated PTM entries using the same filters as the web interface.

4.1 POST /search_ptm_data

Example request body (multiple filters):
POST https://prix.hanyang.ac.kr/strucptm/api/search_ptm_data
Content-Type: application/json

{
  "pdb_id_chain": "132L:A",
  "annotation": "Methylation",
  "organism": "Chicken",
  "assembly_type": ["Monomer", "Multimer"],
  "secondary_structure": ["H", "E"],
  "rsa_min": 0.2,
  "rsa_max": 1.0
}
Example (PowerShell)
$body = @'
{
  "pdb_id_chain": "132L:A",
  "annotation": "Methylation",
  "organism": "Chicken",
  "assembly_type": ["Monomer", "Multimer"],
  "secondary_structure": ["H", "E"],
  "rsa_min": 0.2,
  "rsa_max": 1.0
}
'@

Invoke-RestMethod -Method Post `
  -Uri "https://prix.hanyang.ac.kr/strucptm/api/search_ptm_data" `
  -ContentType "application/json" `
  -Body $body
Example (curl, bash/Linux/macOS)
curl -X POST "https://prix.hanyang.ac.kr/strucptm/api/search_ptm_data" \
  -H "Content-Type: application/json" \
  -H "Accept: application/json" \
  -d '{   "pdb_id_chain": "132L:A",   "annotation": "Methylation",   "organism": "Chicken",   "assembly_type": ["Monomer", "Multimer"],   "secondary_structure": ["H", "E"],   "rsa_min": 0.2,   "rsa_max": 1.0 }'
Note: On Windows PowerShell, using Invoke-RestMethod is recommended for POST requests to avoid JSON quoting issues. In bash environments, curl is typically the simplest option.

5. Citation

When using StrucPTM in your work, please cite the StrucPTM database paper:
  • “StrucPTM” – main database and curation manuscript. (link to be added after publication)