Research workbench
2.1 a structure of acyl-adenylate synthetase from methanosarcina acetivorans containing a link between LYS256 and CYS298
Analyse 2.1 a structure of acyl-adenylate synthetase from methanosarcina acetivorans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ETC
- Type
- protein
- Length
- 1,068 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMP-binding protein
- EC
- 6.2.1.-
- UniProt
- Q8TLW1
- Ligands
- FOR, MG, NO3
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AMP-binding protein (EC 6.2.1.-) | protein | 531 | 32% helix, 26% strand | Q8TLW1 |
| B | AMP-binding protein (EC 6.2.1.-) | protein | 537 | 32% helix, 26% strand | Q8TLW1 |
Ligands and binding sites
- FOR · Formyl group · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- PGE · Triethylene glycol · additive · 3 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.84 | 0.85 | 107 | EPE, MG |
| 2 | 909 | 0.83 | 0.84 | 79 | PGE, EPE, GOL |
| 3 | 913 | 0.82 | 0.83 | 83 | 1PE, EPE, GOL |
| 4 | 248 | 0.57 | 0.79 | 41 | GOL |
| 5 | 89 | 0.53 | 0.85 | 22 | GOL |
Interfaces
1 interface between chains.
- A–B · 945 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3ETC · 2.1 A structure of acyl-adenylate synthetase from Methanosarcina acetivorans containing a… · 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 Q8TLW1
- Elsewhere: RCSB PDB 3ETC · PDBe 3ETC · UniProt Q8TLW1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.