Research workbench
Adenylation domain of a keto acid-selecting nrps module bound to keto acyl adenylate space group P212121
Analyse Adenylation domain of a keto acid-selecting nrps module bound to keto acyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ULY
- Type
- protein
- Length
- 1,076 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amino acid adenylation domain-containing protein
- UniProt
- M5R382
- Ligands
- QA7, SO4
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amino acid adenylation domain-containing protein | protein | 545 | 36% helix, 26% strand | M5R382 |
| B | Amino acid adenylation domain-containing protein | protein | 531 | 35% helix, 26% strand | M5R382 |
Ligands and binding sites
- QA7 · 5'-O-{(S)-hydroxy[(4-methyl-2-oxopentanoyl) oxy]phosphoryl}adenosine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 21 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
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 | 828 | 0.78 | 0.81 | 78 | QA7, SO4 |
| 2 | 1070 | 0.78 | 0.80 | 108 | SO4, QA7 |
| 3 | 276 | 0.67 | 0.83 | 37 | SO4, GOL |
| 4 | 283 | 0.61 | 0.79 | 44 | empty |
| 5 | 138 | 0.57 | 0.83 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1854 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6ULY · Adenylation domain of a keto acid-selecting NRPS module bound to keto acyl adenylate… · 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 M5R382
- Elsewhere: RCSB PDB 6ULY · PDBe 6ULY · UniProt M5R382
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