MolNFT v1 · #163774 · protein
Crystal structure of the catalytic domain of human NUDT12 in complex with 7-methyl-guanosine-5'-triphosphate
6SCX · Peroxisomal NADH pyrophosphatase NUDT12: “Crystal structure of the catalytic domain of human NUDT12 in complex with 7-methyl-guanosine-5'-triphosphate”. X-ray diffraction, 2 ligands (MGP, CD), 18 pockets (best druggability 0.80).…
- PDB
- 6SCX
- Type
- protein
- Length
- 976 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisomal NADH pyrophosphatase NUDT12
- EC
- 3.6.1.22
- UniProt
- Q9BQG2
- Ligands
- MGP, CD
- Pockets
- 18 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisomal NADH pyrophosphatase NUDT12 (EC 3.6.1.22) | protein | 328 | 30% helix, 28% strand | Q9BQG2 |
| B | Peroxisomal NADH pyrophosphatase NUDT12 (EC 3.6.1.22) | protein | 325 | 30% helix, 28% strand | Q9BQG2 |
| C | Peroxisomal NADH pyrophosphatase NUDT12 (EC 3.6.1.22) | protein | 323 | 30% helix, 28% strand | Q9BQG2 |
Ligands and binding sites
- MGP · 7-methyl-guanosine-5'-triphosphate · ligand · 3 copies · chains A, B, C
- CD · Cadmium ion · metal · 9 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.80 | 0.82 | 75 | CD, MGP |
| 2 | 740 | 0.76 | 0.81 | 59 | CD, MGP |
| 3 | 776 | 0.76 | 0.80 | 66 | CD |
| 4 | 204 | 0.57 | 0.80 | 26 | empty |
| 5 | 255 | 0.55 | 0.76 | 37 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2527 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 1271 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6SCX · Crystal structure of the catalytic domain of human NUDT12 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BQG2 · AlphaFold monomer V2.0 prediction for NAD-capped RNA hydrolase NUDT12 (Q9BQG2) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9BQG2
- Elsewhere: RCSB PDB 6SCX · PDBe 6SCX · UniProt Q9BQG2
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