MolNFT v1 · #104761 · protein
Crystal structure of human ALKBH7 in complex with alpha-ketoglutarate and MN(II)
4QKD · Alpha-ketoglutarate-dependent dioxygenase alkb homolog 7…: “Crystal structure of human ALKBH7 in complex with alpha-ketoglutarate and MN(II)”. X-ray diffraction, 2 ligands (AKG, MN), 10 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 4QKD
- Type
- protein
- Length
- 568 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-ketoglutarate-dependent dioxygenase alkb homolog 7, mitochondrial
- EC
- 1.14.11.-
- UniProt
- Q9BT30
- Ligands
- AKG, MN
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-ketoglutarate-dependent dioxygenase alkb homolog 7, mitochondrial (EC 1.14.11.-) | protein | 190 | 23% helix, 39% strand | Q9BT30 |
| C | Alpha-ketoglutarate-dependent dioxygenase alkb homolog 7, mitochondrial (EC 1.14.11.-) | protein | 188 | 23% helix, 38% strand | Q9BT30 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 3 copies · chains A, C, B
- MN · Manganese (II) ion · metal · 7 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.78 | 0.80 | 97 | MN, AKG |
| 2 | 159 | 0.47 | 0.77 | 30 | empty |
| 3 | 157 | 0.46 | 0.76 | 28 | empty |
| 4 | 154 | 0.43 | 0.75 | 24 | empty |
| 5 | 116 | 0.41 | 0.76 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 535 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 532 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 523 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nonstandard).
Compared structures
- 4QKD · Crystal structure of human ALKBH7 in complex with alpha-ketoglutarate and Mn(II) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BT30 · AlphaFold monomer V2.0 prediction for alpha-ketoglutarate-dependent dioxygenase alkb… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9BT30
- Elsewhere: RCSB PDB 4QKD · PDBe 4QKD · UniProt Q9BT30
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