Research workbench
Structure of the tetrahydromethanopterin dependent formaldehyde- activating enzyme (fae) from methylobacterium extorquens AM1 with bound 5,10-methylene tetrahydromethanopterin
Analyse Structure of the tetrahydromethanopterin dependent formaldehyde- activating… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y60
- Type
- protein
- Length
- 841 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Formaldehyde-activating enzyme fae
- UniProt
- Q9FA38
- Ligands
- H4M
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | Formaldehyde-activating enzyme fae | protein | 168 | 42% helix, 23% strand | Q9FA38 |
| D | Formaldehyde-activating enzyme fae | protein | 169 | 42% helix, 22% strand | Q9FA38 |
Ligands and binding sites
- H4M · 5,10-dimethylene tetrahydromethanopterin · ligand · 5 copies · chains B, C, A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.77 | 0.94 | 30 | empty |
| 2 | 417 | 0.70 | 0.81 | 39 | H4M |
| 3 | 419 | 0.70 | 0.81 | 38 | H4M |
| 4 | 411 | 0.69 | 0.81 | 37 | H4M |
| 5 | 424 | 0.68 | 0.80 | 38 | H4M |
Interfaces
5 interfaces between chains.
- C–D · 1856 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1846 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 1826 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1823 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1821 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1Y60 · Structure of the tetrahydromethanopterin dependent formaldehyde-activating enzyme (Fae)… · the same entry in another collection · chain E against E, TM-score 1.00
- Q9FA38 · AlphaFold monomer V2.0 prediction for 5,6,7,8-tetrahydromethanopterin hydro-lyase (Q9FA38) · 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 Q9FA38
- Elsewhere: RCSB PDB 1Y60 · PDBe 1Y60 · UniProt Q9FA38
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