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
- 2FHK
- 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, K
- Pockets
- 14 · best druggability 0.77
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 · 3 copies · chains A, B, C, D
- K · Potassium ion · metal · 18 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 581 | 0.77 | 0.83 | 68 | K |
| 2 | 76 | 0.77 | 0.99 | 16 | empty |
| 3 | 74 | 0.74 | 0.98 | 17 | empty |
| 4 | 485 | 0.74 | 0.82 | 56 | MFN |
| 5 | 437 | 0.73 | 0.82 | 53 | MFN |
Interfaces
6 interfaces between chains.
- C–D · 3037 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 3015 Ų buried · 51 hydrogen bonds · protein-protein
- B–C · 889 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 883 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 351 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2FHK · Crystal structure of formylmethanofuran: tetrahydromethanopterin formyltransferase in… · the same entry in another collection · chain D against D, TM-score 1.00
- Q49610 · AlphaFold monomer V2.0 prediction for formylmethanofuran-- tetrahydromethanopterin… · a predicted model of the same protein · chain B 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 2FHK · PDBe 2FHK · UniProt Q49610
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