Research workbench
Human O6-alkylguanine-DNA alkyltransferase covalently crosslinked to DNA
Analyse Human O6-alkylguanine-DNA alkyltransferase covalently crosslinked to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T39
- Type
- protein + DNA
- Length
- 351 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*CP*CP*AP*TP*GP*(E1X)P*CP*TP*AP*GP*TP*A)- 3'…
- EC
- 2.1.1.63
- UniProt
- P16455
- Pockets
- 5 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | 5'-D(*GP*CP*CP*AP*TP*GP*(E1X)P*CP*TP*AP*GP*TP*A)- 3' | dna | 13 | — | — |
| D, F | 5'-D(*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3' | dna | 13 | — | — |
| A | Methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63) | protein | 151 | 42% helix, 14% strand | P16455 |
| B | Methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63) | protein | 148 | 43% helix, 11% strand | P16455 |
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.48 | 0.81 | 16 | empty |
| 2 | 87 | 0.47 | 0.82 | 17 | empty |
| 3 | 90 | 0.45 | 0.81 | 21 | empty |
| 4 | 63 | 0.41 | 0.82 | 18 | empty |
| 5 | 65 | 0.31 | 0.75 | 11 | empty |
Interfaces
9 interfaces between chains.
- E–B · 621 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–A · 611 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–D · 556 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- E–F · 543 Ų buried · 38 hydrogen bonds · nucleic-nucleic
- F–B · 314 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1T39 · Human O6-alkylguanine-DNA alkyltransferase covalently crosslinked to DNA · the same entry in another collection · chain B against B, TM-score 1.00
- P16455 · AlphaFold monomer V2.0 prediction for methylated-DNA--protein- cysteine methyltransferase… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P16455
- Elsewhere: RCSB PDB 1T39 · PDBe 1T39 · UniProt P16455
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