MolNFT v1 · #141886 · protein + DNA
Crystal structure of fto in complex with M6DA modified ssdna
5ZMD · Alpha-ketoglutarate-dependent dioxygenase fto: “Crystal structure of fto in complex with M6DA modified ssdna”. X-ray diffraction, 2 ligands (OGA, MN), 20 pockets (best druggability 0.76). MolNFT v1 #141886 on GenesisL1: 3D…
- PDB
- 5ZMD
- Type
- protein + DNA
- Length
- 1,631 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-ketoglutarate-dependent dioxygenase fto; DNA…
- EC
- 1.14.11.-
- UniProt
- Q9C0B1
- Ligands
- OGA, MN
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent dioxygenase fto (EC 1.14.11.-) | protein | 402 | 40% helix, 21% strand | Q9C0B1 |
| B, D, F, H | DNA (5'-D(P*TP*CP*TP*(6MA)P*TP*AP*TP*CP*G)-3') | dna | 9 | — | — |
| C | Alpha-ketoglutarate-dependent dioxygenase fto (EC 1.14.11.-) | protein | 395 | 39% helix, 21% strand | Q9C0B1 |
| E | Alpha-ketoglutarate-dependent dioxygenase fto (EC 1.14.11.-) | protein | 395 | 37% helix, 22% strand | Q9C0B1 |
| G | Alpha-ketoglutarate-dependent dioxygenase fto (EC 1.14.11.-) | protein | 403 | 37% helix, 21% strand | Q9C0B1 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 4 copies · chains A, B, C, E, F, G, H
- MN · Manganese (II) ion · metal · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.76 | 0.99 | 26 | MN, OGA |
| 2 | 80 | 0.76 | 0.98 | 25 | MN, OGA |
| 3 | 64 | 0.74 | 0.99 | 23 | OGA |
| 4 | 551 | 0.72 | 0.81 | 61 | empty |
| 5 | 65 | 0.72 | 0.97 | 22 | MN, OGA |
Interfaces
12 interfaces between chains.
- A–C · 1171 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1077 Ų buried · 23 hydrogen bonds · protein-nucleic
- E–G · 1076 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1049 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 979 Ų buried · 20 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide, 4 modified (disulfide, nucleotide modification).
Compared structures
- 5ZMD · Crystal structure of FTO in complex with m6dA modified ssDNA · the same entry in another collection · chain H against H, TM-score 1.00
- Q9C0B1 · AlphaFold monomer V2.0 prediction for alpha-ketoglutarate-dependent dioxygenase fto… · a predicted model of the same protein · chain C 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 Q9C0B1
- Elsewhere: RCSB PDB 5ZMD · PDBe 5ZMD · UniProt Q9C0B1
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