Research workbench
Formyl-COA:OXALATE CoA-transferase from acetobacter aceti
Analyse Formyl-COA:OXALATE CoA-transferase from acetobacter aceti in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UBM
- Type
- protein
- Length
- 1,717 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formyl-COA:OXALATE CoA-transferase
- EC
- 2.8.3.-
- UniProt
- A9X6P7
- Ligands
- COA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formyl-COA:OXALATE CoA-transferase (EC 2.8.3.-) | protein | 428 | 38% helix, 14% strand | A9X6P7 |
| B, D | Formyl-COA:OXALATE CoA-transferase (EC 2.8.3.-) | protein | 430 | 37% helix, 14% strand | A9X6P7 |
| C | Formyl-COA:OXALATE CoA-transferase (EC 2.8.3.-) | protein | 429 | 37% helix, 14% strand | A9X6P7 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, B, C, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 916 | 0.82 | 0.84 | 97 | COA |
| 2 | 1026 | 0.81 | 0.82 | 114 | COA |
| 3 | 854 | 0.79 | 0.82 | 109 | COA |
| 4 | 805 | 0.78 | 0.82 | 93 | COA |
| 5 | 126 | 0.69 | 0.90 | 31 | empty |
Interfaces
5 interfaces between chains.
- C–D · 6597 Ų buried · 67 hydrogen bonds · protein-protein
- A–B · 6497 Ų buried · 67 hydrogen bonds · protein-protein
- A–D · 455 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 397 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 33 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3UBM · Formyl-CoA:oxalate CoA-transferase from Acetobacter aceti · 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 A9X6P7
- Elsewhere: RCSB PDB 3UBM · PDBe 3UBM · UniProt A9X6P7
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