Research workbench
Crystal structure of ALKBH1 in complex with MN(II) and N-oxalylglycine
Analyse Crystal structure of ALKBH1 in complex with MN(II) and N-oxalylglycine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IMC
- Type
- protein
- Length
- 1,357 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleic acid dioxygenase ALKBH1
- EC
- 1.14.11.-, 1.14.11.51, 4.2.99.18, 1.14.11.33
- UniProt
- P0CB42
- Ligands
- OGA, MN
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Nucleic acid dioxygenase ALKBH1 (EC 1.14.11.-, 1.14.11.51, 4.2.99.18, 1.14.11.33) | protein | 339 | 28% helix, 23% strand | P0CB42 |
| D | Nucleic acid dioxygenase ALKBH1 (EC 1.14.11.-, 1.14.11.51, 4.2.99.18, 1.14.11.33) | protein | 340 | 28% helix, 22% strand | P0CB42 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.80 | 0.82 | 99 | empty |
| 2 | 900 | 0.77 | 0.80 | 95 | empty |
| 3 | 244 | 0.70 | 0.85 | 36 | empty |
| 4 | 231 | 0.63 | 0.82 | 33 | MN, OGA |
| 5 | 241 | 0.63 | 0.82 | 37 | OGA |
Interfaces
6 interfaces between chains.
- A–C · 644 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 617 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 504 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 371 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 199 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6IMC · Crystal Structure of ALKBH1 in complex with Mn(II) and N-Oxalylglycine · the same entry in another collection · chain D against D, TM-score 1.00
- P0CB42 · AlphaFold monomer V2.0 prediction for nucleic acid dioxygenase ALKBH1 (P0CB42) · 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 P0CB42
- Elsewhere: RCSB PDB 6IMC · PDBe 6IMC · UniProt P0CB42
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