MolNFT v1 · #188368 · protein
X-ray crystal structure of glycerol dibiphytanyl glycerol tetraether - macrocyclic archaeol synthase (gdgt-mas) from methanocaldococcus jannaschii with archaeal lipid, 5'DEOXYADENOSINE, and methionine bound
7TOL: “X-ray crystal structure of glycerol dibiphytanyl glycerol tetraether - macrocyclic archaeol synthase…”. X-ray diffraction, 6 ligands (SF4, 5AD, MET), 4 pockets (best druggability 0.90). MolNFT v1 #188368 on GenesisL1: 3D structure…
- PDB
- 7TOL
- Type
- protein
- Length
- 493 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerol dibiphytanyl glycerol tetraether - macrocyclic archaeol synthase
- EC
- 2.1.1.-
- UniProt
- Q58036
- Ligands
- SF4, 5AD, MET, L1P, L4P, FE
- Pockets
- 4 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol dibiphytanyl glycerol tetraether - macrocyclic archaeol synthase (EC 2.1.1.-) | protein | 493 | 40% helix, 21% strand | Q58036 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A
- 5AD · 5'-deoxyadenosine · ligand · chains A
- MET · Methionine · ligand · chains A
- L1P · 3-phosphoryl-[1,2-di-phytanyl]glycerol · ligand · chains A
- L4P · 3-[glycerolylphosphonyl]-[1,2-di-phytanyl]glycerol · ligand · chains A
- FE · Fe (III) ion · metal · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.90 | 0.91 | 108 | SF4, 5AD, MET, L1P, L4P |
| 2 | 168 | 0.49 | 0.77 | 31 | empty |
| 3 | 59 | 0.44 | 0.83 | 18 | empty |
| 4 | 58 | 0.30 | 0.75 | 15 | empty |
Compared structures
- 7TOL · X-ray crystal structure of glycerol dibiphytanyl glycerol tetraether - macrocyclic… · the same entry in another collection · chain A against A, TM-score 1.00
- Q58036 · AlphaFold monomer V2.0 prediction for 7,8-dihydro-6-hydroxymethylpterin… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q58036
- Elsewhere: RCSB PDB 7TOL · PDBe 7TOL · UniProt Q58036
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