MolNFT v1 · #122067 · protein
Crystal structure of the bacillus-conserved mazg protein, a nucleotide pyrophosphohydrolase
5IE9: “Crystal structure of the bacillus-conserved mazg protein, a nucleotide pyrophosphohydrolase”. X-ray diffraction, 1 ligand (MN), 4 pockets (best druggability 0.46). MolNFT v1 #122067 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5IE9
- Type
- protein
- Length
- 375 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleotide pyrophosphohydrolase
- UniProt
- A0A0A3VU53
- Ligands
- MN
- Pockets
- 4 · best druggability 0.46
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nucleotide pyrophosphohydrolase | protein | 94 | 72% helix, 1% strand | A0A0A3VU53 |
| C | Nucleotide pyrophosphohydrolase | protein | 95 | 69% helix, 1% strand | A0A0A3VU53 |
| D | Nucleotide pyrophosphohydrolase | protein | 92 | 71% helix, 1% strand | A0A0A3VU53 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.46 | 0.79 | 13 | empty |
| 2 | 102 | 0.44 | 0.78 | 15 | empty |
| 3 | 109 | 0.42 | 0.76 | 18 | empty |
| 4 | 88 | 0.38 | 0.76 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2356 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 2348 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 545 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 466 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 221 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5IE9 · Crystal structure of the Bacillus-conserved MazG protein, a nucleotide… · 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 A0A0A3VU53
- Elsewhere: RCSB PDB 5IE9 · PDBe 5IE9 · UniProt A0A0A3VU53
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