MolNFT v1 · #87821 · protein
60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with MN(II) and N-oxalylglycine (nog)
4CCK · Bifunctional lysine-specific demethylase and histidyl…: “60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with MN(II) and N-oxalylglycine (nog)”. X-ray diffraction, 2 ligands (OGA, MN), 18 pockets (best druggability…
- PDB
- 4CCK
- Type
- protein
- Length
- 1,829 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional lysine-specific demethylase and histidyl- hydroxylase NO66
- EC
- 1.14.11.-, 1.14.11.27
- UniProt
- Q9H6W3
- Ligands
- OGA, MN
- Pockets
- 18 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bifunctional lysine-specific demethylase and histidyl- hydroxylase NO66 (EC 1.14.11.-, 1.14.11.27) | protein | 456 | 38% helix, 21% strand | Q9H6W3 |
| C | Bifunctional lysine-specific demethylase and histidyl- hydroxylase NO66 (EC 1.14.11.-, 1.14.11.27) | protein | 458 | 38% helix, 21% strand | Q9H6W3 |
| D | Bifunctional lysine-specific demethylase and histidyl- hydroxylase NO66 (EC 1.14.11.-, 1.14.11.27) | protein | 459 | 37% helix, 21% strand | Q9H6W3 |
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
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1144 | 0.75 | 0.78 | 131 | MN, OGA, EDO |
| 2 | 286 | 0.72 | 0.86 | 47 | empty |
| 3 | 253 | 0.71 | 0.86 | 42 | empty |
| 4 | 233 | 0.70 | 0.86 | 38 | empty |
| 5 | 750 | 0.69 | 0.76 | 82 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3400 Ų buried · 52 hydrogen bonds · protein-protein
- C–D · 3335 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 1287 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1243 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4CCK · 60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II) and… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9H6W3 · AlphaFold monomer V2.0 prediction for ribosomal oxygenase 1 (Q9H6W3) · a predicted model of the same protein · chain C against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 4CCK · PDBe 4CCK · UniProt Q9H6W3
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