Research workbench
Crystal structure of the ADP-binding domain of the NAD+ riboswitch with nicotinamide adenine dinucleotide (NAD+)
Analyse Crystal structure of the ADP-binding domain of the NAD+ riboswitch with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TFF
- Type
- RNA
- Length
- 52 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chains: a
- Ligands
- NAD, MG, NA, BR
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chains: a | rna | 52 | — | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- MG · Magnesium ion · metal · 5 copies · chains A
- NA · Sodium ion · metal · chains A
- BR · Bromide ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.53 | 0.72 | 25 | BR |
| 2 | 51 | 0.22 | 0.72 | 11 | MG, BR |
Compared structures
- 6TFF · Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Nicotinamide… · 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
- Elsewhere: RCSB PDB 6TFF · PDBe 6TFF
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