Research workbench
Crystal structure of class II aars homologue (BLL0957) complexed with AMP
Analyse Crystal structure of class II aars homologue (BLL0957) complexed with AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MF2
- Type
- protein
- Length
- 595 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BLL0957 protein
- UniProt
- Q89VT8
- Ligands
- AMP, ZN
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BLL0957 protein | protein | 299 | 40% helix, 27% strand | Q89VT8 |
| B | BLL0957 protein | protein | 296 | 39% helix, 27% strand | Q89VT8 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 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 | 613 | 0.78 | 0.84 | 48 | empty |
| 2 | 576 | 0.77 | 0.84 | 55 | ZN, AMP |
| 3 | 555 | 0.76 | 0.83 | 53 | AMP |
Interfaces
1 interface between chains.
- A–B · 2594 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3MF2 · Crystal structure of class II aaRS homologue (Bll0957) complexed with AMP · 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 3MF2 · PDBe 3MF2 · UniProt Q89VT8
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