Research workbench
Crystal structure of the cptin type III toxin-antitoxin system from eubacterium rectale
Analyse Crystal structure of the cptin type III toxin-antitoxin system from eubacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RMO
- Type
- protein + RNA
- Length
- 1,600 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cptn toxin; RNA (45-mer)
- UniProt
- D6E269
- Ligands
- CA
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O | Cptn toxin | protein | 155 | 34% helix, 26% strand | D6E269 |
| B, D, F, H, J, L, N, P | RNA (45-mer) | rna | 45 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 48 copies · chains A, F, B, E, D, C, H, G, I, L, J, K, M, P, N, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.71 | 0.81 | 44 | CA |
| 2 | 691 | 0.69 | 0.77 | 66 | empty |
| 3 | 255 | 0.64 | 0.83 | 31 | CA |
| 4 | 279 | 0.63 | 0.82 | 28 | CA |
| 5 | 291 | 0.62 | 0.81 | 32 | CA |
Interfaces
28 interfaces between chains.
- E–F · 1351 Ų buried · 39 hydrogen bonds · protein-nucleic
- I–J · 1324 Ų buried · 44 hydrogen bonds · protein-nucleic
- K–L · 1311 Ų buried · 41 hydrogen bonds · protein-nucleic
- C–D · 1310 Ų buried · 38 hydrogen bonds · protein-nucleic
- M–N · 1310 Ų buried · 43 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 48 modified (engineered, nucleotide modification).
Compared structures
- 4RMO · Crystal Structure of the CptIN Type III Toxin-Antitoxin System from Eubacterium rectale · 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 D6E269
- Elsewhere: RCSB PDB 4RMO · PDBe 4RMO · UniProt D6E269
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