Research workbench
Structure of the codh component of the M. barkeri acds complex
Analyse Structure of the codh component of the M. barkeri acds complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CF4
- Type
- protein
- Length
- 935 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl-CoA DECARBOXYLASE/SYNTHASE alpha subunit; Acetyl-CoA DECARBOXYLASE/SYNTHASE…
- EC
- 1.2.99.2
- Ligands
- SF4, WCC, FE, CMO
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetyl-CoA DECARBOXYLASE/SYNTHASE alpha subunit (EC 1.2.99.2) | protein | 766 | 46% helix, 12% strand | — |
| G | Acetyl-CoA DECARBOXYLASE/SYNTHASE epsilon subunit (EC 1.2.99.2) | protein | 169 | 37% helix, 14% strand | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A
- WCC · FE(3)-NI(1)-S(4) cluster · ligand · chains A
- FE · Fe (III) ion · metal · chains A
- CMO · Carbon monoxide · ion · chains A
- ACY · Acetic acid · additive · 11 copies · chains A, G
- GOL · Glycerol · additive · 3 copies · chains A, G
- PEG · Di(hydroxyethyl)ether · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.77 | 0.97 | 38 | WCC, CMO |
| 2 | 538 | 0.69 | 0.79 | 55 | ACY, GOL |
| 3 | 386 | 0.67 | 0.80 | 39 | empty |
| 4 | 267 | 0.66 | 0.83 | 39 | ACY |
| 5 | 143 | 0.50 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–G · 2106 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 3CF4 · Structure of the CODH component of the M. barkeri ACDS complex · 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
- Elsewhere: RCSB PDB 3CF4 · PDBe 3CF4
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