Research workbench
Glutaconyl-CoA decarboxylase a subunit from clostridium symbiosum co- crystallized with glutaryl-CoA
Analyse Glutaconyl-CoA decarboxylase a subunit from clostridium symbiosum co… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GMA
- Type
- protein
- Length
- 1,124 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutaconyl-CoA decarboxylase subunit a
- EC
- 4.1.1.70
- UniProt
- B7TVP1
- Ligands
- GRA
- Pockets
- 13 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutaconyl-CoA decarboxylase subunit a (EC 4.1.1.70) | protein | 558 | 42% helix, 18% strand | B7TVP1 |
| B | Glutaconyl-CoA decarboxylase subunit a (EC 4.1.1.70) | protein | 566 | 43% helix, 18% strand | B7TVP1 |
Ligands and binding sites
- GRA · glutaryl-coenzyme A · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.70 | 0.80 | 74 | empty |
| 2 | 139 | 0.53 | 0.81 | 31 | empty |
| 3 | 120 | 0.50 | 0.80 | 26 | empty |
| 4 | 143 | 0.48 | 0.78 | 30 | empty |
| 5 | 109 | 0.48 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1921 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3GMA · Glutaconyl-coA decarboxylase A subunit from Clostridium symbiosum co-crystallized 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 B7TVP1
- Elsewhere: RCSB PDB 3GMA · PDBe 3GMA · UniProt B7TVP1
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