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Crystal structure of a putative polyketide cyclase (TM1040_3560) from silicibacter sp. TM1040 at 2.00 a resolution
Analyse Crystal structure of a putative polyketide cyclase (TM1040_3560) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F8H
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative polyketide cyclase
- UniProt
- Q1GLD7
- Ligands
- CA
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative polyketide cyclase | protein | 137 | 28% helix, 46% strand | Q1GLD7 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 6 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.77 | 0.87 | 38 | MRD, ACT |
| 2 | 636 | 0.77 | 0.83 | 62 | MPD, MRD, ACT |
| 3 | 108 | 0.52 | 0.82 | 26 | empty |
| 4 | 59 | 0.37 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1412 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3F8H · Crystal structure of a putative polyketide cyclase (tm1040_3560) from silicibacter sp.… · 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 Q1GLD7
- Elsewhere: RCSB PDB 3F8H · PDBe 3F8H · UniProt Q1GLD7
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