MolNFT v1 · #104762 · protein
Crystal structure of human ALKBH7 in complex with N-oxalylglycine and MN(II)
4QKF · Alpha-ketoglutarate-dependent dioxygenase alkb homolog 7…: “Crystal structure of human ALKBH7 in complex with N-oxalylglycine and MN(II)”. X-ray diffraction, 2 ligands (OGA, MN), 9 pockets (best druggability 0.77). MolNFT v1 #104762…
- PDB
- 4QKF
- Type
- protein
- Length
- 570 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
- OGA, MN
- Pockets
- 9 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Alpha-ketoglutarate-dependent dioxygenase alkb homolog 7, mitochondrial (EC 1.14.11.-) | protein | 190 | 23% helix, 39% strand | Q9BT30 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, C, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.77 | 0.80 | 93 | MN, OGA |
| 2 | 237 | 0.59 | 0.80 | 43 | empty |
| 3 | 123 | 0.47 | 0.79 | 25 | empty |
| 4 | 62 | 0.43 | 0.82 | 16 | empty |
| 5 | 163 | 0.43 | 0.75 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 589 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 576 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 546 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4QKF · Crystal structure of human ALKBH7 in complex with N-oxalylglycine 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 B 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 4QKF · PDBe 4QKF · UniProt Q9BT30
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