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
- 4HH4
- Type
- protein
- Length
- 1,519 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ccbj
- UniProt
- E9JES0
- Ligands
- SAH, SO4
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ccbj | protein | 254 | 30% helix, 34% strand | E9JES0 |
| B, D, F | Ccbj | protein | 251 | 31% helix, 34% strand | E9JES0 |
| C, E | Ccbj | protein | 256 | 30% helix, 34% strand | E9JES0 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 20 copies · chains A, F, B, C, D, E
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D, E
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 457 | 0.81 | 0.88 | 67 | SAH, GOL |
| 2 | 435 | 0.80 | 0.88 | 63 | SAH, GOL |
| 3 | 703 | 0.80 | 0.84 | 80 | SAH, SO4, GOL |
| 4 | 663 | 0.79 | 0.84 | 74 | SAH |
| 5 | 707 | 0.78 | 0.83 | 77 | SAH, SO4, GOL |
Interfaces
12 interfaces between chains.
- B–C · 803 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 785 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 750 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 747 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 746 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4HH4 · Structure of the CcbJ Methyltransferase from Streptomyces caelestis · the same entry in another collection · chain B against B, 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 4HH4 · PDBe 4HH4 · UniProt E9JES0
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