MolNFT v1 · #88747 · protein
Mutant P250A of bacterial chalcone isomerase from eubacterium ramulus
4D4F: “Mutant P250A of bacterial chalcone isomerase from eubacterium ramulus”. X-ray diffraction, 1 ligand (CL), 15 pockets (best druggability 0.87). MolNFT v1 #88747 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4D4F
- Type
- protein
- Length
- 1,580 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chalcone isomerase
- EC
- 5.5.1.6
- UniProt
- V9P0A9
- Ligands
- CL
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chalcone isomerase (EC 5.5.1.6) | protein | 262 | 31% helix, 23% strand | V9P0A9 |
| B, E | Chalcone isomerase (EC 5.5.1.6) | protein | 259 | 31% helix, 24% strand | V9P0A9 |
| C | Chalcone isomerase (EC 5.5.1.6) | protein | 260 | 30% helix, 23% strand | V9P0A9 |
| D | Chalcone isomerase (EC 5.5.1.6) | protein | 258 | 31% helix, 24% strand | V9P0A9 |
| F | Chalcone isomerase (EC 5.5.1.6) | protein | 282 | 30% helix, 23% strand | V9P0A9 |
Ligands and binding sites
- CL · Chloride ion · ion · 16 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 11 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.87 | 0.93 | 78 | empty |
| 2 | 515 | 0.86 | 0.93 | 80 | empty |
| 3 | 372 | 0.82 | 0.91 | 53 | empty |
| 4 | 365 | 0.81 | 0.90 | 47 | empty |
| 5 | 366 | 0.80 | 0.90 | 48 | empty |
Interfaces
12 interfaces between chains.
- A–B · 2218 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2205 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2197 Ų buried · 32 hydrogen bonds · protein-protein
- D–F · 1002 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 976 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4D4F · Mutant P250A of bacterial chalcone isomerase from Eubacterium ramulus · 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 V9P0A9
- Elsewhere: RCSB PDB 4D4F · PDBe 4D4F · UniProt V9P0A9
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