MolNFT v1 · #152571 · protein
Crystal structure of ALKBH1 without alpha-1 (N37-C369)
6IMA · Nucleic acid dioxygenase ALKBH1: “Crystal structure of ALKBH1 without alpha-1 (N37-C369)”. X-ray diffraction, 13 pockets (best druggability 0.70). MolNFT v1 #152571 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IMA
- Type
- protein
- Length
- 863 residues
- Chains
- 3
- 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
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleic acid dioxygenase ALKBH1 (EC 1.14.11.-, 1.14.11.51, 4.2.99.18, 1.14.11.33) | protein | 297 | 24% helix, 22% strand | P0CB42 |
| B | Nucleic acid dioxygenase ALKBH1 (EC 1.14.11.-, 1.14.11.51, 4.2.99.18, 1.14.11.33) | protein | 284 | 20% helix, 24% strand | P0CB42 |
| C | Nucleic acid dioxygenase ALKBH1 (EC 1.14.11.-, 1.14.11.51, 4.2.99.18, 1.14.11.33) | protein | 282 | 26% helix, 23% strand | P0CB42 |
Ligands and binding sites
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.70 | 0.77 | 64 | empty |
| 2 | 668 | 0.69 | 0.77 | 62 | empty |
| 3 | 549 | 0.69 | 0.78 | 53 | empty |
| 4 | 215 | 0.56 | 0.79 | 29 | empty |
| 5 | 152 | 0.49 | 0.78 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–B · 851 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 803 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
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 6IMA · PDBe 6IMA · UniProt P0CB42
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