MolNFT v1 · #98683 · protein
Crystal structure of a putative polyketide cyclase (CV_0247) from chromobacterium violaceum atcc 12472 at 2.72 a resolution
4LGQ: “Crystal structure of a putative polyketide cyclase (CV_0247) from chromobacterium violaceum atcc 12472 at…”. X-ray diffraction, 1 ligand (CL), 3 pockets (best druggability 0.85). MolNFT v1 #98683 on GenesisL1: 3D structure, binding…
- PDB
- 4LGQ
- Type
- protein
- Length
- 536 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative polyketide cyclase
- UniProt
- Q7P1G6
- Ligands
- CL
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative polyketide cyclase | protein | 134 | 34% helix, 43% strand | Q7P1G6 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.85 | 0.86 | 115 | PEG, EDO, CL |
| 2 | 422 | 0.74 | 0.83 | 44 | CL, PG4 |
| 3 | 393 | 0.73 | 0.83 | 45 | CL, PEG, EDO |
Interfaces
4 interfaces between chains.
- A–B · 1004 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 990 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 398 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 134 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 4LGQ · Crystal structure of a putative polyketide cyclase (CV_0247) from Chromobacterium… · 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 Q7P1G6
- Elsewhere: RCSB PDB 4LGQ · PDBe 4LGQ · UniProt Q7P1G6
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