MolNFT v1 · #87825 · protein
60S ribosomal protein L8 histidine hydroxylase (NO66 S373C) in complex with MN(II), N-oxalylglycine (nog) and 60S ribosomal protein L8 (RPL8 G214C) peptide fragment (complex-3)
4CCO · Bifunctional lysine-specific demethylase and histidyl…: “60S ribosomal protein L8 histidine hydroxylase (NO66 S373C) in complex with MN(II), N-oxalylglycine (nog) and…”. X-ray diffraction, 2 ligands (OGA, MN), 7 pockets (best…
- PDB
- 4CCO
- Type
- protein
- Length
- 941 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional lysine-specific demethylase and histidyl- hydroxylase NO66; 60S ribosomal…
- EC
- 1.14.11.-, 1.14.11.27
- UniProt
- Q9H6W3, P62917
- Ligands
- OGA, MN
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional lysine-specific demethylase and histidyl- hydroxylase NO66 (EC 1.14.11.-, 1.14.11.27) | protein | 458 | 38% helix, 21% strand | Q9H6W3 |
| B | Bifunctional lysine-specific demethylase and histidyl- hydroxylase NO66 (EC 1.14.11.-, 1.14.11.27) | protein | 459 | 38% helix, 22% strand | Q9H6W3 |
| C, D | 60S ribosomal protein L8 | protein | 12 | 0% helix, 0% strand | P62917 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, C, B, D
- MN · Manganese (II) ion · metal · 2 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.75 | 0.99 | 22 | MN, OGA |
| 2 | 66 | 0.74 | 0.99 | 23 | MN, OGA |
| 3 | 420 | 0.70 | 0.81 | 58 | EDO |
| 4 | 246 | 0.67 | 0.84 | 36 | EDO |
| 5 | 94 | 0.48 | 0.81 | 17 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 3316 Ų buried · 54 hydrogen bonds · protein-protein
- A–C · 784 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 747 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4CCO · 60S ribosomal protein L8 histidine hydroxylase (NO66 S373C) in complex with Mn(II)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H6W3 · AlphaFold monomer V2.0 prediction for ribosomal oxygenase 1 (Q9H6W3) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P62917 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L8 (P62917) · a predicted model of the same protein · chain C against A, TM-score 0.27
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 Q9H6W3
- Every structure of UniProt P62917
- Elsewhere: RCSB PDB 4CCO · PDBe 4CCO · UniProt Q9H6W3 · UniProt P62917
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