Research workbench
Crystal structure of a mycobacterial protein
Analyse Crystal structure of a mycobacterial protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D6J
- Type
- protein
- Length
- 704 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA synthase; Ubiquitin-like protein SMT3
- UniProt
- A0R618, Q12306
- Ligands
- ATP, MG
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA synthase | protein | 630 | 33% helix, 24% strand | A0R618 |
| B | Ubiquitin-like protein SMT3 | protein | 74 | 18% helix, 38% strand | Q12306 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.81 | 0.82 | 106 | MG, ATP |
| 2 | 216 | 0.63 | 0.82 | 20 | empty |
| 3 | 87 | 0.45 | 0.81 | 17 | empty |
| 4 | 147 | 0.43 | 0.75 | 28 | empty |
| 5 | 94 | 0.43 | 0.79 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 396 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- Q12306 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein SMT3 (Q12306) · a predicted model of the same protein · chain B against A, TM-score 0.98
- A0R618 · AlphaFold monomer V2.0 prediction for long-chain-fatty-acid--AMP ligase FADD32 (A0R618) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 A0R618
- Every structure of UniProt Q12306
- Elsewhere: RCSB PDB 5D6J · PDBe 5D6J · UniProt A0R618 · UniProt Q12306
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