Research workbench
Structure of coproheme decarboxylase from corynebacterium dipththeriae W183Y mutant in complex with coproheme
Analyse Structure of coproheme decarboxylase from corynebacterium dipththeriae W183Y… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q4F
- Type
- protein
- Length
- 1,150 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coproheme decarboxylase from corynebacterium dipththeriae W183Y mutant in complex with…
- UniProt
- A0A2T1BSE4
- Ligands
- FEC
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Coproheme decarboxylase from corynebacterium dipththeriae W183Y mutant in complex with coproheme | protein | 230 | 33% 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 · 2 copies · chains B, E
- PGE · Triethylene glycol · additive · chains A, C
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 | 612 | 0.78 | 0.84 | 52 | FEC |
| 2 | 583 | 0.77 | 0.83 | 51 | FEC |
| 3 | 584 | 0.77 | 0.83 | 51 | FEC |
| 4 | 555 | 0.76 | 0.83 | 50 | FEC |
| 5 | 525 | 0.76 | 0.83 | 48 | FEC |
Interfaces
5 interfaces between chains.
- D–E · 1534 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1527 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1507 Ų buried · 22 hydrogen bonds · protein-protein
- B–E · 1479 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1472 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 7Q4F · Structure of coproheme decarboxylase from Corynebacterium dipththeriae W183Y 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 7Q4F · PDBe 7Q4F · UniProt A0A2T1BSE4
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