Research workbench
Structure of coproheme decarboxylase from corynebacterium diphteriae in complex with monovinyl monopropionyl deuteroheme
Analyse Structure of coproheme decarboxylase from corynebacterium diphteriae in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XUB
- Type
- protein
- Length
- 1,142 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chlorite dismutase
- UniProt
- A0A2T1BSE4
- Ligands
- VOV
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Chlorite dismutase | protein | 230 | 33% helix, 28% strand | A0A2T1BSE4 |
| B | Chlorite dismutase | protein | 231 | 33% helix, 28% strand | A0A2T1BSE4 |
| D | Chlorite dismutase | protein | 228 | 32% helix, 28% strand | A0A2T1BSE4 |
| E | Chlorite dismutase | protein | 223 | 31% helix, 29% strand | A0A2T1BSE4 |
Ligands and binding sites
- VOV · harderoheme (III) · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 541 | 0.77 | 0.84 | 52 | VOV |
| 2 | 504 | 0.76 | 0.84 | 53 | VOV |
| 3 | 498 | 0.76 | 0.84 | 51 | VOV |
| 4 | 539 | 0.75 | 0.83 | 51 | VOV |
| 5 | 511 | 0.74 | 0.82 | 48 | VOV |
Interfaces
5 interfaces between chains.
- A–C · 1534 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1496 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 1487 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1487 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1483 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6XUB · Structure of coproheme decarboxylase from Corynebacterium diphteriae in complex with… · 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 A0A2T1BSE4
- Elsewhere: RCSB PDB 6XUB · PDBe 6XUB · UniProt A0A2T1BSE4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.