Research workbench
60S ribosomal protein L27A histidine hydroxylase (MINA53) in complex with NI(II) and 2-oxoglutarate (2OG)
Analyse 60S ribosomal protein L27A histidine hydroxylase (MINA53) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BU2
- Type
- protein
- Length
- 379 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional lysine-specific demethylase and histidyl- hydroxylase mina
- EC
- 1.14.11.-
- UniProt
- Q8IUF8
- Ligands
- AKG, NI
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional lysine-specific demethylase and histidyl- hydroxylase mina (EC 1.14.11.-) | protein | 379 | 36% helix, 22% strand | Q8IUF8 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- NI · Nickel (II) ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.68 | 0.95 | 17 | NI, AKG |
| 2 | 376 | 0.57 | 0.75 | 52 | EDO |
| 3 | 52 | 0.30 | 0.76 | 13 | empty |
| 4 | 51 | 0.25 | 0.73 | 12 | EDO |
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4BU2 · 60S ribosomal protein L27A histidine hydroxylase (MINA53) in complex with Ni(II) and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IUF8 · AlphaFold monomer V2.0 prediction for ribosomal oxygenase 2 (Q8IUF8) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q8IUF8
- Elsewhere: RCSB PDB 4BU2 · PDBe 4BU2 · UniProt Q8IUF8
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