Research workbench
Crystal structure of a cyclase filc from fischerella sp. in complex with 4-(1H-indol-3-YL)BUTAN-2-one
Analyse Crystal structure of a cyclase filc from fischerella sp. in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZFJ
- Type
- protein
- Length
- 796 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyclase
- UniProt
- A0A1P8VSI6
- Ligands
- 9BF, CA
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Acyclase | protein | 199 | 0% helix, 45% strand | A0A1P8VSI6 |
Ligands and binding sites
- 9BF · 4-(1~{H}-indol-3-yl)butan-2-one · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B, D
- GOL · Glycerol · additive · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.85 | 0.93 | 54 | 9BF |
| 2 | 243 | 0.71 | 0.86 | 30 | 9BF |
| 3 | 216 | 0.69 | 0.86 | 27 | 9BF |
| 4 | 118 | 0.67 | 0.90 | 25 | empty |
| 5 | 106 | 0.64 | 0.89 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 921 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 912 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 869 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5ZFJ · Crystal structure of a cyclase Filc from Fischerella sp. in complex with… · 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 A0A1P8VSI6
- Elsewhere: RCSB PDB 5ZFJ · PDBe 5ZFJ · UniProt A0A1P8VSI6
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