MolNFT v1 · #51852 · protein
Formyl-CoA transferase mutant variant Q17A with aspartyl-CoA thioester intermediates and oxalate
2VJO · Formyl-coenzyme a transferase: “Formyl-CoA transferase mutant variant Q17A with aspartyl-CoA thioester intermediates and oxalate”. X-ray diffraction, 3 ligands (COA, OXL, CL), 13 pockets (best druggability 0.77). MolNFT v1 #51852 on…
- PDB
- 2VJO
- Type
- protein
- Length
- 854 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formyl-coenzyme a transferase
- EC
- 2.8.3.16
- UniProt
- O06644
- Ligands
- COA, OXL, CL
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Formyl-coenzyme a transferase (EC 2.8.3.16) | protein | 427 | 37% helix, 13% strand | O06644 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, B
- OXL · Oxalate ion · ligand · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.77 | 0.97 | 40 | CL |
| 2 | 385 | 0.75 | 0.85 | 57 | OXL, COA, CL |
| 3 | 66 | 0.72 | 0.98 | 34 | empty |
| 4 | 349 | 0.72 | 0.84 | 41 | COA |
| 5 | 210 | 0.61 | 0.82 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 6233 Ų buried · 77 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2VJO · Formyl-CoA transferase mutant variant Q17A with aspartyl-CoA thioester intermediates and… · the same entry in another collection · chain B against B, TM-score 1.00
- O06644 · AlphaFold monomer V2.0 prediction for formyl-COA:OXALATE CoA- transferase (O06644) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O06644
- Elsewhere: RCSB PDB 2VJO · PDBe 2VJO · UniProt O06644
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