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
- 4HGZ
- Type
- protein
- Length
- 1,406 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ccbj
- UniProt
- E9JES0
- Ligands
- LI, SO4
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 28% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Ccbj | protein | 236 | 28% helix, 36% strand | E9JES0 |
| B | Ccbj | protein | 228 | 29% helix, 37% strand | E9JES0 |
| C | Ccbj | protein | 237 | 29% helix, 36% strand | E9JES0 |
| D | Ccbj | protein | 235 | 28% helix, 37% strand | E9JES0 |
| F | Ccbj | protein | 234 | 26% helix, 37% strand | E9JES0 |
Ligands and binding sites
- LI · Lithium ion · metal · 2 copies · chains C, D, E, F
- SO4 · Sulfate ion · ion · 8 copies · chains A, E, B, D, C, F
- EDO · 1,2-ethanediol · additive · 4 copies · chains B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.74 | 0.77 | 79 | empty |
| 2 | 1065 | 0.71 | 0.75 | 88 | SO4 |
| 3 | 949 | 0.71 | 0.75 | 74 | empty |
| 4 | 919 | 0.71 | 0.76 | 67 | empty |
| 5 | 891 | 0.69 | 0.75 | 65 | empty |
Interfaces
11 interfaces between chains.
- C–D · 859 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 858 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 847 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 635 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 631 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4HGZ · Structure of the CcbJ Methyltransferase from Streptomyces caelestis · the same entry in another collection · chain A 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 E9JES0
- Elsewhere: RCSB PDB 4HGZ · PDBe 4HGZ · UniProt E9JES0
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