Research workbench
Glutaconyl-CoA decarboxylase a subunit from clostridium symbiosum co- crystallized with crotonyl-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
- 3GLM
- Type
- protein
- Length
- 2,244 residues
- Chains
- 4
- 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
- COO, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Glutaconyl-CoA decarboxylase subunit a (EC 4.1.1.70) | protein | 562 | 42% helix, 18% strand | B7TVP1 |
| C | Glutaconyl-CoA decarboxylase subunit a (EC 4.1.1.70) | protein | 558 | 42% helix, 18% strand | B7TVP1 |
Ligands and binding sites
- COO · Crotonyl coenzyme A · ligand · 4 copies · chains A, C, B, D
- CL · Chloride ion · ion · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.82 | 0.87 | 107 | empty |
| 2 | 605 | 0.81 | 0.87 | 47 | empty |
| 3 | 592 | 0.81 | 0.86 | 41 | empty |
| 4 | 124 | 0.70 | 0.90 | 25 | empty |
| 5 | 129 | 0.67 | 0.88 | 24 | empty |
Interfaces
6 interfaces between chains.
- B–D · 4496 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 4361 Ų buried · 54 hydrogen bonds · protein-protein
- A–D · 1894 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1891 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1419 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 3GLM · Glutaconyl-coA decarboxylase A subunit from Clostridium symbiosum co-crystallized with… · the same entry in another collection · chain C against C, 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 3GLM · PDBe 3GLM · UniProt B7TVP1
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