Research workbench
Structure of the ccbj methyltransferase from streptomyces caelestis
Analyse Structure of the ccbj methyltransferase from streptomyces caelestis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HGY
- Type
- protein
- Length
- 1,407 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ccbj
- UniProt
- E9JES0
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ccbj | protein | 238 | 26% helix, 36% strand | E9JES0 |
| B | Ccbj | protein | 229 | 28% helix, 37% strand | E9JES0 |
| C | Ccbj | protein | 234 | 27% helix, 37% strand | E9JES0 |
| D, F | Ccbj | protein | 235 | 27% helix, 36% strand | E9JES0 |
| E | Ccbj | protein | 236 | 27% helix, 37% strand | E9JES0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 11 copies · chains A, E, B, D, C, F
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.74 | 0.77 | 66 | empty |
| 2 | 991 | 0.73 | 0.76 | 80 | empty |
| 3 | 925 | 0.72 | 0.76 | 66 | empty |
| 4 | 953 | 0.72 | 0.76 | 66 | SO4 |
| 5 | 556 | 0.69 | 0.78 | 50 | empty |
Interfaces
11 interfaces between chains.
- A–F · 850 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 848 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 842 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 640 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 635 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4HGY · Structure of the CcbJ Methyltransferase from Streptomyces caelestis · the same entry in another collection · chain C against C, 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 E9JES0
- Elsewhere: RCSB PDB 4HGY · PDBe 4HGY · UniProt E9JES0
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