Research workbench
Ydiu complex with ampnpp and MN2+
Analyse Ydiu complex with ampnpp and MN2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LNA
- Type
- protein
- Length
- 927 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein adenylyltransferase selo
- EC
- 2.7.7.-
- UniProt
- A0A024L327
- Ligands
- ANP, MN, CA
- Pockets
- 11 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein adenylyltransferase selo (EC 2.7.7.-) | protein | 463 | 45% helix, 15% strand | A0A024L327 |
| B | Protein adenylyltransferase selo (EC 2.7.7.-) | protein | 464 | 45% helix, 15% strand | A0A024L327 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.64 | 0.77 | 43 | MN, ANP |
| 2 | 427 | 0.63 | 0.78 | 45 | MN, ANP |
| 3 | 391 | 0.57 | 0.75 | 38 | empty |
| 4 | 374 | 0.56 | 0.74 | 40 | empty |
| 5 | 73 | 0.39 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 360 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6LNA · YdiU complex with AMPNPP and Mn2+ · 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 A0A024L327
- Elsewhere: RCSB PDB 6LNA · PDBe 6LNA · UniProt A0A024L327
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