MolNFT v1 · #156405 · protein
Structural and functional insights into an archaeal synthase
6M34 · Digeranylgeranylglyceryl phosphate synthase: “Structural and functional insights into an archaeal synthase”. X-ray diffraction, 4 ligands (MPG, DMA, MG), 4 pockets (best druggability 0.70). MolNFT v1 #156405 on GenesisL1: 3D…
- PDB
- 6M34
- Type
- protein
- Length
- 560 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Digeranylgeranylglyceryl phosphate synthase
- EC
- 2.5.1.42
- UniProt
- Q57727
- Ligands
- MPG, DMA, MG, PO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 80% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Digeranylgeranylglyceryl phosphate synthase (EC 2.5.1.42) | protein | 280 | 80% helix, 1% strand | Q57727 |
Ligands and binding sites
- MPG · [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate · ligand · 4 copies · chains A, B
- DMA · Dimethylallyl diphosphate · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- LDA · Lauryl dimethylamine-N-oxide · additive · chains B
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 | 482 | 0.70 | 0.80 | 51 | DMA, MG |
| 2 | 488 | 0.70 | 0.80 | 50 | LDA |
| 3 | 394 | 0.57 | 0.73 | 33 | empty |
| 4 | 74 | 0.29 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6M34 · Structural and functional insights into an Archaeal synthase · the same entry in another collection · chain A against A, TM-score 1.00
- Q57727 · AlphaFold monomer V2.0 prediction for digeranylgeranylglyceryl phosphate synthase (Q57727) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 Q57727
- Elsewhere: RCSB PDB 6M34 · PDBe 6M34 · UniProt Q57727
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