Research workbench
Crystal structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in complex with its coenzymes
Analyse Crystal structure of formylmethanofuran: tetrahydromethanopterin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FHJ
- Type
- protein
- Length
- 1,184 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formylmethanofuran--tetrahydromethanopterin formyltransferase
- EC
- 2.3.1.101
- UniProt
- Q49610
- Ligands
- MFN, H4Z, K
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Formylmethanofuran--tetrahydromethanopterin formyltransferase (EC 2.3.1.101) | protein | 296 | 27% helix, 35% strand | Q49610 |
Ligands and binding sites
- MFN · N-[4,5,7-tricarboxyheptanoyl]-L-gamma-glutamyl-N-{2-[4-({5-[(formylamino)methyl]-3-furyl}methoxy) phenyl]ethyl}-D-glutamine · ligand · 4 copies · chains A, B, C, D
- H4Z · 5-(4-{[1-(2-amino-5-formyl-7-methyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl)ethyl]amino}phenyl)-5-deoxy-1-O-{5-O-[(1,3-dicarboxypropoxy)(hydroxy)phosphoryl]pentofuranosyl}pentitol · ligand · 2 copies · chains A, C
- K · Potassium ion · metal · 17 copies · chains A, B, C, D
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 3 copies · chains A, B, C, D
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 636 | 0.82 | 0.86 | 81 | PE3, PE4 |
| 2 | 84 | 0.75 | 0.97 | 18 | PE4 |
| 3 | 299 | 0.74 | 0.87 | 44 | empty |
| 4 | 75 | 0.74 | 0.97 | 17 | empty |
| 5 | 497 | 0.74 | 0.82 | 55 | MFN |
Interfaces
6 interfaces between chains.
- C–D · 3014 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 2983 Ų buried · 52 hydrogen bonds · protein-protein
- A–D · 856 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 818 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 354 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 2FHJ · Crystal structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in… · the same entry in another collection · chain C against C, TM-score 1.00
- Q49610 · AlphaFold monomer V2.0 prediction for formylmethanofuran-- tetrahydromethanopterin… · 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 Q49610
- Elsewhere: RCSB PDB 2FHJ · PDBe 2FHJ · UniProt Q49610
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