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Structure of coproheme decarboxylase from Corynebacterium dipththeriae Y135A mutant in complex with coproheme
Analyse Structure of coproheme decarboxylase from Corynebacterium dipththeriae Y135A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q4G
- Type
- protein
- Length
- 1,149 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.82
- Source
- Corynebacterium diphtheriae
- Molecule
- Coproheme decarboxylase from Corynebacterium diphtheriae Y135A mutant in complex with…
- UniProt
- A0A2T1BSE4
- Ligands
- FEC
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.82 · 3 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Coproheme decarboxylase from Corynebacterium diphtheriae Y135A mutant in complex with coproheme | protein | 230 | 33% helix, 28% strand | A0A2T1BSE4 |
| C | Coproheme decarboxylase from Corynebacterium diphtheriae Y135A mutant in complex with coproheme | protein | 231 | 33% helix, 28% strand | A0A2T1BSE4 |
| E | Coproheme decarboxylase from Corynebacterium diphtheriae Y135A mutant in complex with coproheme | protein | 228 | 30% helix, 28% strand | A0A2T1BSE4 |
Ligands and binding sites
- FEC · 1,3,5,8-tetramethyl-porphine-2,4,6,7-tetrapropionic acid ferrous complex · ligand · 5 copies · chains A, B, C, D, E
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.78 | 0.84 | 57 | FEC |
| 2 | 557 | 0.77 | 0.84 | 61 | FEC |
| 3 | 575 | 0.77 | 0.84 | 58 | FEC |
| 4 | 553 | 0.77 | 0.84 | 55 | FEC |
| 5 | 569 | 0.77 | 0.83 | 53 | FEC |
Interfaces
5 interfaces between chains.
- A–C · 1537 Ų buried · 23 hydrogen bonds · protein-protein
- B–E · 1524 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1511 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1493 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1469 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 7Q4G · Structure of coproheme decarboxylase from corynebacterium dipththeriae Y135A mutant in… · 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 7Q4G · PDBe 7Q4G · UniProt A0A2T1BSE4
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