MolNFT v1 · #28479 · protein + DNA
Wt human O6-alkylguanine-DNA alkyltransferase bound to DNA containing an alkylated cytosine
1YFH · 5'-D(*GP*TP*GP*GP*AP*TP*GP*(XCY)…: “Wt human O6-alkylguanine-DNA alkyltransferase bound to DNA containing an alkylated cytosine”. X-ray diffraction, 1 ligand (ZN), 12 pockets (best druggability 0.53). MolNFT v1 #28479 on GenesisL1…
- PDB
- 1YFH
- Type
- protein + DNA
- Length
- 539 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*TP*GP*GP*AP*TP*GP*(XCY) P*GP*TP*GP*TP*AP*GP*GP*T)-3'; 5'…
- EC
- 2.1.1.63
- UniProt
- P16455
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.53
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, F | 5'-D(*GP*TP*GP*GP*AP*TP*GP*(XCY) P*GP*TP*GP*TP*AP*GP*GP*T)-3' | dna | 16 | — | — |
| E, G | 5'- D(*CP*CP*TP*AP*CP*AP*CP*AP*CP*AP*TP*CP*CP*AP*CP*A)-3' | dna | 16 | — | — |
| A | Methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63) | protein | 165 | 37% helix, 17% strand | P16455 |
| B | Methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63) | protein | 161 | 38% helix, 18% strand | P16455 |
| C | Methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63) | protein | 149 | 42% helix, 18% strand | P16455 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.53 | 0.81 | 19 | empty |
| 2 | 261 | 0.53 | 0.76 | 32 | empty |
| 3 | 86 | 0.49 | 0.82 | 15 | empty |
| 4 | 95 | 0.48 | 0.81 | 15 | empty |
| 5 | 122 | 0.47 | 0.79 | 22 | empty |
Interfaces
9 interfaces between chains.
- F–A · 752 Ų buried · 12 hydrogen bonds · protein-nucleic
- D–E · 696 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- F–G · 677 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- D–C · 629 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 564 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1YFH · wt Human O6-Alkylguanine-DNA Alkyltransferase Bound To DNA Containing an Alkylated… · the same entry in another collection · chain C against C, TM-score 1.00
- P16455 · AlphaFold monomer V2.0 prediction for methylated-DNA--protein- cysteine methyltransferase… · a predicted model of the same protein · chain C 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 P16455
- Elsewhere: RCSB PDB 1YFH · PDBe 1YFH · UniProt P16455
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