Research workbench
Crystal structure of TRIS/PPIX2/MG2+ bound form of cyclolavandulyl diphosphate synthase (clds) from streptomyces sp. CL190
Analyse Crystal structure of TRIS/PPIX2/MG2+ bound form of cyclolavandulyl diphosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GUL
- Type
- protein
- Length
- 864 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclolavandulyl diphosphate synthase
- UniProt
- X5IYJ5
- Ligands
- POP, MG
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cyclolavandulyl diphosphate synthase | protein | 216 | 49% helix, 15% strand | X5IYJ5 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 8 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.78 | 0.98 | 26 | POP, MG, TRS |
| 2 | 105 | 0.78 | 0.98 | 28 | POP, MG, TRS |
| 3 | 103 | 0.77 | 0.97 | 27 | POP, MG, TRS |
| 4 | 84 | 0.75 | 0.97 | 27 | POP, MG, TRS |
| 5 | 655 | 0.71 | 0.78 | 62 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2232 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2208 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 315 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 286 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 170 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5GUL · Crystal structure of Tris/PPix2/Mg2+ bound form of cyclolavandulyl diphosphate synthase… · 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 X5IYJ5
- Elsewhere: RCSB PDB 5GUL · PDBe 5GUL · UniProt X5IYJ5
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