MolNFT v1 · #36993 · protein + RNA
Methionyl-trnafmet formyltransferase complexed with formyl-methionyl- trnafmet
2FMT · Formyl-methionyl-TRNAFMET2: “Methionyl-trnafmet formyltransferase complexed with formyl-methionyl- trnafmet”. X-ray diffraction, 2 ligands (FME, MG), 11 pockets (best druggability 0.80). MolNFT v1 #36993 on GenesisL1: 3D structure…
- PDB
- 2FMT
- Type
- protein + RNA
- Length
- 782 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formyl-methionyl-TRNAFMET2; Methionyl-tRNA fmet formyltransferase
- EC
- 2.1.2.9
- UniProt
- P23882
- Ligands
- FME, MG
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | Formyl-methionyl-TRNAFMET2 | rna | 77 | — | — |
| A, B | Methionyl-tRNA fmet formyltransferase (EC 2.1.2.9) | protein | 314 | 30% helix, 27% strand | P23882 |
Ligands and binding sites
- FME · N-formylmethionine · ligand · 2 copies · chains C, A, D, B
- MG · Magnesium ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.80 | 0.82 | 115 | FME |
| 2 | 1063 | 0.75 | 0.78 | 76 | MG |
| 3 | 543 | 0.70 | 0.79 | 71 | FME |
| 4 | 532 | 0.63 | 0.76 | 39 | empty |
| 5 | 448 | 0.59 | 0.75 | 23 | empty |
Interfaces
4 interfaces between chains.
- C–A · 1517 Ų buried · 40 hydrogen bonds · protein-nucleic
- D–B · 1499 Ų buried · 34 hydrogen bonds · protein-nucleic
- A–B · 391 Ų buried · 4 hydrogen bonds · protein-protein
- C–B · 156 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 10 modified, 2 covalent (nucleotide modification, covalent ligand).
Compared structures
- 2FMT · Methionyl-trnafmet formyltransferase complexed with formyl-methionyl-trnafmet · the same entry in another collection · chain C against C, TM-score 1.00
- P23882 · AlphaFold monomer V2.0 prediction for methionyl-tRNA formyltransferase (P23882) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P23882
- Elsewhere: RCSB PDB 2FMT · PDBe 2FMT · UniProt P23882
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