Research workbench
60S ribosomal protein L27A histidine hydroxylase (MINA53 Y209C) in complex with MN(II), 2-oxoglutarate (2OG) and 60S ribosomal protein L27A (RPL27A G37C) peptide fragment
Analyse 60S ribosomal protein L27A histidine hydroxylase (MINA53 Y209C) 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
- 4BXF
- Type
- protein
- Length
- 864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional lysine-specific demethylase and histidyl- hydroxylase mina; 60S ribosomal…
- EC
- 1.14.11.-
- UniProt
- Q8IUF8, P46776
- Ligands
- AKG, MN
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional lysine-specific demethylase and histidyl- hydroxylase mina (EC 1.14.11.-) | protein | 425 | 33% helix, 23% strand | Q8IUF8 |
| B | Bifunctional lysine-specific demethylase and histidyl- hydroxylase mina (EC 1.14.11.-) | protein | 422 | 33% helix, 23% strand | Q8IUF8 |
| C | 60S ribosomal protein L27A | protein | 9 | 0% helix, 0% strand | P46776 |
| D | 60S ribosomal protein L27A | protein | 8 | 0% helix, 0% strand | P46776 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, C, B
- MN · Manganese (II) ion · metal · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.76 | 0.99 | 23 | MN, AKG |
| 2 | 111 | 0.75 | 0.95 | 22 | empty |
| 3 | 71 | 0.75 | 0.98 | 20 | MN, AKG |
| 4 | 143 | 0.70 | 0.90 | 28 | empty |
| 5 | 86 | 0.47 | 0.82 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3523 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 731 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 695 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4BXF · 60S ribosomal protein L27A histidine hydroxylase (MINA53 Y209C) in complex with MN(II)… · 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 0.99
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 Q8IUF8
- Every structure of UniProt P46776
- Elsewhere: RCSB PDB 4BXF · PDBe 4BXF · UniProt Q8IUF8 · UniProt P46776
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