Research workbench
Structure of the ubid-class enzyme hmff from pelotomaculum thermopropionicum in complex with FMN
Analyse Structure of the ubid-class enzyme hmff from pelotomaculum thermopropionicum in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H6V
- Type
- protein
- Length
- 2,670 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases
- UniProt
- A5D4Z9
- Ligands
- FMN, K, MN, CA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases | protein | 445 | 29% helix, 27% strand | A5D4Z9 |
| D | 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases | protein | 444 | 29% helix, 27% strand | A5D4Z9 |
| F | 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases | protein | 446 | 28% helix, 27% strand | A5D4Z9 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- K · Potassium ion · metal · 6 copies · chains A, B, C, D, E, F
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.83 | 0.84 | 62 | empty |
| 2 | 881 | 0.82 | 0.84 | 77 | FMN, K |
| 3 | 511 | 0.81 | 0.88 | 57 | empty |
| 4 | 505 | 0.81 | 0.88 | 56 | empty |
| 5 | 516 | 0.81 | 0.87 | 59 | empty |
Interfaces
12 interfaces between chains.
- B–C · 3481 Ų buried · 51 hydrogen bonds · protein-protein
- A–E · 3452 Ų buried · 53 hydrogen bonds · protein-protein
- D–F · 3429 Ų buried · 57 hydrogen bonds · protein-protein
- E–F · 1156 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 1106 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 6H6V · Structure of the UbiD-class enzyme HmfF from Pelotomaculum thermopropionicum in complex… · the same entry in another collection · chain A 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 A5D4Z9
- Elsewhere: RCSB PDB 6H6V · PDBe 6H6V · UniProt A5D4Z9
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