MolNFT v1 · #96323 · protein + DNA
Human tdg N140A mutant in a complex with 5-carboxylcytosine (5CAC)
4JGC · G/T mismatch-specific thymine DNA glycosylase: “Human tdg N140A mutant in a complex with 5-carboxylcytosine (5CAC)”. X-ray diffraction, 2 ligands (ORP, 1RT), 2 pockets (best druggability 0.74). MolNFT v1 #96323 on GenesisL1: 3D…
- PDB
- 4JGC
- Type
- protein + DNA
- Length
- 251 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- G/T mismatch-specific thymine DNA glycosylase; Oligonucleotide; Oligonucleotide…
- EC
- 3.2.2.29
- UniProt
- Q13569
- Ligands
- ORP, 1RT
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | G/T mismatch-specific thymine DNA glycosylase (EC 3.2.2.29) | protein | 196 | 41% helix, 13% strand | Q13569 |
| C | Oligonucleotide | dna | 28 | — | — |
| D | Oligonucleotide containing 5-carboxylcytosine | dna | 27 | — | — |
Ligands and binding sites
- ORP · 2-deoxy-5-phosphono-ribose · ligand · chains A, D
- 1RT · 4-amino-2-oxo-1,2-dihydropyrimidine-5-carboxylic acid · ligand · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.74 | 0.84 | 54 | ORP, 1RT |
| 2 | 697 | 0.69 | 0.77 | 37 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1234 Ų buried · 142 hydrogen bonds · nucleic-nucleic
- A–D · 573 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–C · 444 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4JGC · Human TDG N140A mutant IN A COMPLEX WITH 5-carboxylcytosine (5caC) · the same entry in another collection · chain A against A, TM-score 1.00
- Q13569 · AlphaFold monomer V2.0 prediction for G/T mismatch-specific thymine DNA glycosylase… · a predicted model of the same protein · chain A against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q13569
- Elsewhere: RCSB PDB 4JGC · PDBe 4JGC · UniProt Q13569
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