MolNFT v1 · #87823 · protein
60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with MN(II), N-oxalylglycine (nog) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-1)
4CCM · Bifunctional lysine-specific demethylase and histidyl…: “60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with MN(II), N-oxalylglycine (nog) and 60S…”. X-ray diffraction, 2 ligands (OGA, MN), 8 pockets (best…
- PDB
- 4CCM
- Type
- protein
- Length
- 935 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
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 36% 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 | 457 | 36% helix, 21% strand | Q9H6W3 |
| B | Bifunctional lysine-specific demethylase and histidyl- hydroxylase NO66 (EC 1.14.11.-, 1.14.11.27) | protein | 459 | 37% helix, 21% strand | Q9H6W3 |
| C | 60S ribosomal protein L8 | protein | 8 | 0% helix, 0% strand | P62917 |
| D | 60S ribosomal protein L8 | protein | 11 | 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 · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.75 | 0.99 | 22 | MN, OGA |
| 2 | 68 | 0.74 | 0.99 | 22 | MN, OGA |
| 3 | 248 | 0.71 | 0.87 | 43 | empty |
| 4 | 222 | 0.65 | 0.84 | 38 | empty |
| 5 | 117 | 0.51 | 0.81 | 21 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 3303 Ų buried · 55 hydrogen bonds · protein-protein
- B–D · 769 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 704 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4CCM · 60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II)… · the same entry in another collection · chain D against D, 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 0.38
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 4CCM · PDBe 4CCM · UniProt Q9H6W3 · UniProt P62917
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