Research workbench
Crystal structure of putative snoal-like polyketide cyclase (YP_001182657.1) from shewanella putrefaciens cn-32 at 1.44 a resolution
Analyse Crystal structure of putative snoal-like polyketide cyclase (YP_001182657.1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GZB
- Type
- protein
- Length
- 1,164 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative snoal-like polyketide cyclase
- UniProt
- A4Y4H5
- Pockets
- 18 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Putative snoal-like polyketide cyclase | protein | 154 | 29% helix, 44% strand | A4Y4H5 |
| B, D, F, H | Putative snoal-like polyketide cyclase | protein | 137 | 33% helix, 42% strand | A4Y4H5 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 29 copies · chains A, B, C, D, E, F, G, H
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 11 copies · chains A, C, E, G
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 copies · chains A, B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.68 | 0.85 | 27 | MPD, EDO |
| 2 | 159 | 0.68 | 0.87 | 22 | MPD, EDO |
| 3 | 258 | 0.68 | 0.83 | 26 | MRD |
| 4 | 253 | 0.67 | 0.83 | 24 | MRD |
| 5 | 207 | 0.67 | 0.84 | 25 | MPD, EDO |
Interfaces
7 interfaces between chains.
- A–C · 1027 Ų buried · 28 hydrogen bonds · protein-protein
- E–G · 1026 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 724 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 720 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 717 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 modified (engineered).
Compared structures
- 3GZB · Crystal structure of putative SnoaL-like polyketide cyclase (YP_001182657.1) from… · 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 A4Y4H5
- Elsewhere: RCSB PDB 3GZB · PDBe 3GZB · UniProt A4Y4H5
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