MolNFT v1 · #14317 · protein
FORMYLMETHANOFURAN:TETRAHYDROMETHANOPTERIN formyltransferase from archaeoglobus fulgidus
1M5H · Formylmethanofuran--tetrahydromethanopterin…: “FORMYLMETHANOFURAN:TETRAHYDROMETHANOPTERIN formyltransferase from archaeoglobus fulgidus”. X-ray diffraction, 1 ligand (K), 20 pockets (best druggability 0.83). MolNFT v1 #14317 on…
- PDB
- 1M5H
- Type
- protein
- Length
- 2,376 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formylmethanofuran--tetrahydromethanopterin formyltransferase
- EC
- 2.3.1.101
- UniProt
- O28076
- Ligands
- K
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Formylmethanofuran--tetrahydromethanopterin formyltransferase (EC 2.3.1.101) | protein | 297 | 29% helix, 33% strand | O28076 |
Ligands and binding sites
- K · Potassium ion · metal · 24 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.83 | 0.84 | 83 | K |
| 2 | 816 | 0.80 | 0.83 | 66 | K |
| 3 | 637 | 0.80 | 0.85 | 63 | K |
| 4 | 961 | 0.79 | 0.81 | 91 | empty |
| 5 | 594 | 0.76 | 0.82 | 55 | empty |
Interfaces
15 interfaces between chains.
- A–B · 3268 Ų buried · 56 hydrogen bonds · protein-protein
- C–D · 3221 Ų buried · 52 hydrogen bonds · protein-protein
- G–H · 3221 Ų buried · 52 hydrogen bonds · protein-protein
- E–F · 3217 Ų buried · 54 hydrogen bonds · protein-protein
- B–C · 891 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1M5H · Formylmethanofuran:tetrahydromethanopterin formyltransferase from Archaeoglobus fulgidus · the same entry in another collection · chain H against H, TM-score 1.00
- O28076 · AlphaFold monomer V2.0 prediction for formylmethanofuran-- tetrahydromethanopterin… · a predicted model of the same protein · chain B 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 O28076
- Elsewhere: RCSB PDB 1M5H · PDBe 1M5H · UniProt O28076
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