MolNFT v1 · #51850 · protein
Formyl-CoA transferase with aspartyl-formyl anhydide intermediate
2VJM · Formyl-coenzyme a transferase: “Formyl-CoA transferase with aspartyl-formyl anhydide intermediate”. X-ray diffraction, 2 ligands (COA, NA), 13 pockets (best druggability 0.75). MolNFT v1 #51850 on GenesisL1: 3D structure, binding…
- PDB
- 2VJM
- 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, NA
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Formyl-coenzyme a transferase (EC 2.8.3.16) | protein | 427 | 38% helix, 13% strand | O06644 |
| B | Formyl-coenzyme a transferase (EC 2.8.3.16) | protein | 427 | 38% helix, 13% strand | O06644 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- 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 | 86 | 0.75 | 0.98 | 38 | empty |
| 2 | 438 | 0.72 | 0.82 | 53 | COA |
| 3 | 341 | 0.70 | 0.83 | 40 | COA |
| 4 | 227 | 0.62 | 0.82 | 32 | empty |
| 5 | 208 | 0.61 | 0.82 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 6226 Ų buried · 76 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 2VJM · Formyl-CoA transferase with aspartyl-formyl anhydide intermediate · the same entry in another collection · chain A against A, 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 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 O06644
- Elsewhere: RCSB PDB 2VJM · PDBe 2VJM · UniProt O06644
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