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Structure of an evolved dimeric form of the ubid-class enzyme hmff from pelotomaculum thermopropionicum in complex with prfmn
Analyse Structure of an evolved dimeric form of the ubid-class enzyme hmff from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H6X
- Type
- protein
- Length
- 855 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases
- UniProt
- A5D4Z9
- Ligands
- 4LU, K, MN, CA
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases | protein | 427 | 29% helix, 26% strand | A5D4Z9 |
| A | 3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases | protein | 428 | 29% helix, 27% strand | A5D4Z9 |
Ligands and binding sites
- 4LU · 1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-yl)-D-ribitol · ligand · 2 copies · chains B, A
- K · Potassium ion · metal · 2 copies · chains B, A
- MN · Manganese (II) ion · metal · 2 copies · chains B, A
- CA · Calcium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.79 | 0.90 | 45 | empty |
| 2 | 555 | 0.77 | 0.84 | 65 | K, 4LU |
| 3 | 510 | 0.76 | 0.83 | 56 | K, 4LU |
| 4 | 239 | 0.57 | 0.78 | 40 | empty |
| 5 | 89 | 0.50 | 0.83 | 22 | empty |
Interfaces
1 interface between chains.
- B–A · 3123 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 6H6X · Structure of an evolved dimeric form of the UbiD-class enzyme HmfF from Pelotomaculum… · the same entry in another collection · chain B against B, 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 6H6X · PDBe 6H6X · UniProt A5D4Z9
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