MolNFT v1 · #76365 · protein
Histidine 416 of the periplamsic binding protein nika is essential for nickel uptake in escherichia COLI
3QIM · Nickel-binding periplasmic protein: “Histidine 416 of the periplamsic binding protein nika is essential for nickel uptake in escherichia COLI”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.89). MolNFT v1 #76365…
- PDB
- 3QIM
- Type
- protein
- Length
- 996 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nickel-binding periplasmic protein
- UniProt
- P33590
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nickel-binding periplasmic protein | protein | 498 | 32% helix, 25% strand | P33590 |
| B | Nickel-binding periplasmic protein | protein | 498 | 31% helix, 24% strand | P33590 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- ACT · Acetate ion · additive · 13 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.89 | 0.90 | 154 | ACT |
| 2 | 1146 | 0.78 | 0.80 | 68 | GOL, ACT |
| 3 | 1056 | 0.78 | 0.80 | 69 | GOL, ACT, SO4 |
| 4 | 138 | 0.74 | 0.93 | 31 | empty |
| 5 | 58 | 0.55 | 0.89 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1673 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3QIM · Histidine 416 of the periplamsic binding protein NikA is essential for nickel uptake in… · the same entry in another collection · chain A against A, TM-score 1.00
- P33590 · AlphaFold monomer V2.0 prediction for nickel-binding periplasmic protein (P33590) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P33590
- Elsewhere: RCSB PDB 3QIM · PDBe 3QIM · UniProt P33590
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.