MolNFT v1 · #139008 · protein
Structure of mercuric reductase from lysinibacillus sphaericus
5X1Y: “Structure of mercuric reductase from lysinibacillus sphaericus”. X-ray diffraction, 1 ligand (FAD), 20 pockets (best druggability 0.85). MolNFT v1 #139008 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5X1Y
- Type
- protein
- Length
- 2,719 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mercuric reductase
- EC
- 1.16.1.1
- UniProt
- D9J041
- Ligands
- FAD
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Mercuric reductase (EC 1.16.1.1) | protein | 454 | 32% helix, 23% strand | D9J041 |
| A, C, D, E, F | Mercuric reductase (EC 1.16.1.1) | protein | 453 | 32% helix, 23% strand | D9J041 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains B, C, A, E, D, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 472 | 0.85 | 0.92 | 61 | empty |
| 2 | 311 | 0.84 | 0.95 | 47 | empty |
| 3 | 332 | 0.83 | 0.93 | 46 | empty |
| 4 | 1138 | 0.81 | 0.82 | 117 | FAD |
| 5 | 965 | 0.81 | 0.82 | 96 | FAD |
Interfaces
5 interfaces between chains.
- B–C · 3289 Ų buried · 29 hydrogen bonds · protein-protein
- A–E · 3262 Ų buried · 30 hydrogen bonds · protein-protein
- D–F · 3259 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 922 Ų buried · 7 hydrogen bonds · protein-protein
- B–A · 876 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5X1Y · Structure of mercuric reductase from Lysinibacillus sphaericus · 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 D9J041
- Elsewhere: RCSB PDB 5X1Y · PDBe 5X1Y · UniProt D9J041
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.