Research workbench
Crystal structure of class II aars homologue (BLL0957) complexed with an analogue of glycyl adenylate
Analyse Crystal structure of class II aars homologue (BLL0957) complexed with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MF1
- Type
- protein
- Length
- 570 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BLL0957 protein
- UniProt
- Q89VT8
- Ligands
- G5A, ZN
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BLL0957 protein | protein | 295 | 40% helix, 27% strand | Q89VT8 |
| B | BLL0957 protein | protein | 275 | 38% helix, 29% strand | Q89VT8 |
Ligands and binding sites
- G5A · 5'-O-(glycylsulfamoyl)adenosine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.78 | 0.83 | 49 | empty |
| 2 | 568 | 0.77 | 0.84 | 58 | G5A |
| 3 | 398 | 0.68 | 0.81 | 42 | G5A |
Interfaces
1 interface between chains.
- A–B · 2490 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3MF1 · Crystal structure of class II aaRS homologue (Bll0957) complexed with an analogue of… · the same entry in another collection · chain A against A, TM-score 1.00
- Q89VT8 · AlphaFold monomer V2.0 prediction for amino acid--[acyl-carrier- protein] ligase 1… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q89VT8
- Elsewhere: RCSB PDB 3MF1 · PDBe 3MF1 · UniProt Q89VT8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.