MolNFT v1 · #189929 · protein + DNA
Crystal structure of the dioxygenase cctet from coprinopsis cinereain bound to 12BP N6-methyldeoxyadenine (6MA) containing duplex DNA
7W5P: “Crystal structure of the dioxygenase cctet from coprinopsis cinereain bound to 12BP N6-methyldeoxyadenine…”. X-ray diffraction, 2 ligands (OGA, MN), 19 pockets (best druggability 0.76). MolNFT v1 #189929 on GenesisL1: 3D structure…
- PDB
- 7W5P
- Type
- protein + DNA
- Length
- 1,556 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cctet; DNA (12-mer); DNA
- UniProt
- A8P1J0
- Ligands
- OGA, MN
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cctet | protein | 381 | 42% helix, 18% strand | A8P1J0 |
| B, E | DNA (12-mer) | dna | 12 | — | — |
| C, F | DNA | dna | 12 | — | — |
| D | Cctet | protein | 377 | 42% helix, 18% strand | A8P1J0 |
| G | Cctet | protein | 378 | 44% helix, 18% strand | A8P1J0 |
| H | Cctet | protein | 372 | 43% helix, 19% strand | A8P1J0 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 4 copies · chains A, B, D, E, G, H
- MN · Manganese (II) ion · metal · 4 copies · chains A, D, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.76 | 0.81 | 66 | MN, OGA |
| 2 | 489 | 0.72 | 0.82 | 44 | empty |
| 3 | 613 | 0.72 | 0.80 | 45 | empty |
| 4 | 686 | 0.71 | 0.78 | 51 | empty |
| 5 | 397 | 0.67 | 0.80 | 51 | MN, OGA |
Interfaces
14 interfaces between chains.
- A–B · 829 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–E · 802 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 555 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- E–F · 544 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- A–C · 507 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 7W5P · Crystal Structure of the dioxygenase CcTet from Coprinopsis cinereain bound to 12bp… · the same entry in another collection · chain A against A, TM-score 1.00
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 A8P1J0
- Elsewhere: RCSB PDB 7W5P · PDBe 7W5P · UniProt A8P1J0
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