MolNFT v1 · #188369 · protein
X-ray crystal structure of glycerol dibiphytanyl glycerol tetraether - macrocyclic archaeol synthase (gdgt-mas) from methanocaldococcus jannaschii with bacterial lipid substrate analog, 5'DEOXYADENOSINE, and methionine bound
7TOM: “X-ray crystal structure of glycerol dibiphytanyl glycerol tetraether - macrocyclic archaeol synthase…”. X-ray diffraction, 6 ligands (SF4, LPP, 5AD), 4 pockets (best druggability 0.89). MolNFT v1 #188369 on GenesisL1: 3D structure…
- PDB
- 7TOM
- Type
- protein
- Length
- 498 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, LPP, 5AD, MET, FE, SCN
- Pockets
- 4 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerol dibiphytanyl glycerol tetraether - macrocyclic archaeol synthase (EC 2.1.1.-) | protein | 498 | 39% helix, 21% strand | Q58036 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 3 copies · chains A
- LPP · 2-(hexadecanoyloxy)-1-[(phosphonooxy)methyl]ethyl hexadecanoate · ligand · 2 copies · chains A
- 5AD · 5'-deoxyadenosine · ligand · chains A
- MET · Methionine · ligand · chains A
- FE · Fe (III) ion · metal · chains A
- SCN · Thiocyanate ion · ion · 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 | 1179 | 0.89 | 0.90 | 106 | SF4, 5AD, MET, SCN, LPP |
| 2 | 161 | 0.47 | 0.77 | 33 | empty |
| 3 | 60 | 0.33 | 0.77 | 13 | empty |
| 4 | 55 | 0.29 | 0.74 | 14 | empty |
Compared structures
- 7TOM · 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 7TOM · PDBe 7TOM · UniProt Q58036
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