Research workbench
Crystal structure of W200H ubix in complex with a geranyl-FMN N5 adduct
Analyse Crystal structure of W200H ubix in complex with a geranyl-FMN N5 adduct in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QLV
- Type
- protein
- Length
- 2,330 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavin prenyltransferase ubix
- EC
- 2.5.1.129
- UniProt
- A0A072ZCW8
- Ligands
- HZZ, FMN, HJN, NA, PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, H, J, L | Flavin prenyltransferase ubix (EC 2.5.1.129) | protein | 193 | 44% helix, 16% strand | A0A072ZCW8 |
| B | Flavin prenyltransferase ubix (EC 2.5.1.129) | protein | 196 | 44% helix, 15% strand | A0A072ZCW8 |
| D | Flavin prenyltransferase ubix (EC 2.5.1.129) | protein | 195 | 44% helix, 15% strand | A0A072ZCW8 |
| F, G, I | Flavin prenyltransferase ubix (EC 2.5.1.129) | protein | 195 | 44% helix, 15% strand | A0A072ZCW8 |
| K | Flavin prenyltransferase ubix (EC 2.5.1.129) | protein | 196 | 44% helix, 15% strand | A0A072ZCW8 |
Ligands and binding sites
- HZZ · [(2~{Z})-3,7-dimethylocta-2,6-dienyl] dihydrogen phosphate · ligand · 9 copies · chains A, E, J, B, C, H, G, K, L, D, F, I
- FMN · Flavin mononucleotide · ligand · 9 copies · chains A, L, B, I, D, H, E, J, F, K, C, G
- HJN · [(2~{R},3~{S},4~{S})-5-[5-[(2~{Z})-3,7-dimethylocta-2, 6-dienyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate · ligand · 3 copies · chains C, D, I, F, G, E
- NA · Sodium ion · metal · 7 copies · chains B, E, C, H, D, F, G, K, I, J, L
- PO4 · Phosphate ion · ion · 3 copies · chains C, D, I, E, F, G
- ACT · Acetate ion · additive · 7 copies · chains B, C, F, G, H, I, J
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 | 916 | 0.83 | 0.85 | 97 | FMN, ACT, HZZ, NA |
| 2 | 843 | 0.82 | 0.85 | 100 | FMN, HZZ, NA |
| 3 | 871 | 0.82 | 0.84 | 92 | FMN, ACT, HZZ, NA |
| 4 | 362 | 0.74 | 0.85 | 43 | FMN, HZZ |
| 5 | 403 | 0.74 | 0.84 | 41 | HZZ, FMN, ACT |
Interfaces
30 interfaces between chains.
- E–J · 1579 Ų buried · 14 hydrogen bonds · protein-protein
- D–G · 1562 Ų buried · 16 hydrogen bonds · protein-protein
- K–L · 1550 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 1547 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 1545 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6QLV · Crystal structure of W200H UbiX in complex with a geranyl-FMN N5 adduct · 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 A0A072ZCW8
- Elsewhere: RCSB PDB 6QLV · PDBe 6QLV · UniProt A0A072ZCW8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.