Research workbench
Crystal structure of native cymd prenyltransferase
Analyse Crystal structure of native cymd prenyltransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OS3
- Type
- protein
- Length
- 694 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cymd prenyltransferase
- UniProt
- A8M6W6
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cymd prenyltransferase | protein | 350 | 39% helix, 20% strand | A8M6W6 |
| B | Cymd prenyltransferase | protein | 344 | 40% helix, 19% strand | A8M6W6 |
Ligands and binding sites
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.84 | 0.85 | 101 | B3P |
| 2 | 907 | 0.76 | 0.79 | 95 | B3P |
| 3 | 50 | 0.34 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 500 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6OS3 · Crystal structure of native CymD prenyltransferase · 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 A8M6W6
- Elsewhere: RCSB PDB 6OS3 · PDBe 6OS3 · UniProt A8M6W6
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