MolNFT v1 · #163016 · protein
Crystal structure of the iminosuccinate reductase of paracoccus denitrificans in complex with NAD+
6RQA: “Crystal structure of the iminosuccinate reductase of paracoccus denitrificans in complex with NAD+”. X-ray diffraction, 3 ligands (NAD, 7MT, TB), 6 pockets (best druggability 0.73). MolNFT v1 #163016 on GenesisL1: 3D structure…
- PDB
- 6RQA
- Type
- protein
- Length
- 644 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iminosuccinate reductase
- UniProt
- A1B8Z0
- Ligands
- NAD, 7MT, TB
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Iminosuccinate reductase | protein | 322 | 38% helix, 27% strand | A1B8Z0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- 7MT · Tb-Xo4 · ligand · chains B
- TB · Terbium(iii) ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.73 | 0.83 | 54 | NAD |
| 2 | 518 | 0.71 | 0.80 | 53 | NAD |
| 3 | 55 | 0.39 | 0.81 | 19 | empty |
| 4 | 105 | 0.39 | 0.76 | 20 | empty |
| 5 | 62 | 0.38 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2022 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6RQA · Crystal structure of the iminosuccinate reductase of Paracoccus denitrificans in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- A1B8Z0 · AlphaFold monomer V2.0 prediction for iminosuccinate reductase (A1B8Z0) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 A1B8Z0
- Elsewhere: RCSB PDB 6RQA · PDBe 6RQA · UniProt A1B8Z0
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