Research workbench
X-ray structure of the archaeoglobus fulgidus methenyl- tetrahydromethanopterin cyclohydrolase in complex with N5-formyl- tetrahydromethanopterin
Analyse X-ray structure of the archaeoglobus fulgidus methenyl- tetrahydromethanopterin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GVS
- Type
- protein
- Length
- 945 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methenyltetrahydromethanopterin cyclohydrolase
- EC
- 3.5.4.27
- UniProt
- O28344
- Ligands
- F4M
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Methenyltetrahydromethanopterin cyclohydrolase (EC 3.5.4.27) | protein | 315 | 39% helix, 25% strand | O28344 |
Ligands and binding sites
- F4M · 1-[4-({(1R)-1-[(6S,7R)-2-amino-5-formyl-7-methyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]ethyl}amino)phenyl]-1-deoxy-5 -O-{5-O-[(R)-{[(1R)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 899 | 0.73 | 0.77 | 79 | empty |
| 2 | 522 | 0.72 | 0.81 | 44 | empty |
| 3 | 179 | 0.67 | 0.86 | 29 | F4M |
| 4 | 173 | 0.65 | 0.86 | 32 | empty |
| 5 | 191 | 0.53 | 0.78 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1372 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1361 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1338 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4GVS · X-ray structure of the Archaeoglobus fulgidus methenyl-tetrahydromethanopterin… · the same entry in another collection · chain A against A, TM-score 1.00
- O28344 · AlphaFold monomer V2.0 prediction for methenyltetrahydromethanopterin cyclohydrolase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O28344
- Elsewhere: RCSB PDB 4GVS · PDBe 4GVS · UniProt O28344
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