MolNFT v1 · #175979 · protein + RNA
Crystal structure of the DOMAIN1 of NAD+ riboswitch with nicotinamide adenine dinucleotide (NAD+) and U1A protein
7D7V · 17DELU1A (58-mer): “Crystal structure of the DOMAIN1 of NAD+ riboswitch with nicotinamide adenine dinucleotide (NAD+) and U1A…”. X-ray diffraction, 3 ligands (GTP, NAD, MG), 2 pockets (best druggability 0.70). MolNFT v1 #175979 on…
- PDB
- 7D7V
- Type
- protein + RNA
- Length
- 149 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 17DELU1A (58-mer); U1 small nuclear ribonucleoprotein a
- UniProt
- P09012
- Ligands
- GTP, NAD, MG
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 17DELU1A (58-mer) | rna | 57 | — | — |
| C | U1 small nuclear ribonucleoprotein a | protein | 92 | 14% helix, 20% strand | P09012 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- MG · Magnesium ion · metal · 8 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 | 1017 | 0.70 | 0.75 | 42 | MG |
| 2 | 93 | 0.40 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–C · 942 Ų buried · 33 hydrogen bonds · protein-nucleic
Compared structures
- 7D7V · Crystal Structure of the Domain1 of NAD+ Riboswitch with nicotinamide adenine… · the same entry in another collection · chain A against A, TM-score 1.00
- P09012 · AlphaFold monomer V2.0 prediction for U1 small nuclear ribonucleoprotein a (P09012) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 P09012
- Elsewhere: RCSB PDB 7D7V · PDBe 7D7V · UniProt P09012
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