MolNFT v1 · #72135 · protein
X-ray structure of nika in complex with the doubly hydroxylated iron complex, 1-O2
3MZB · Nickel-binding periplasmic protein: “X-ray structure of nika in complex with the doubly hydroxylated iron complex, 1-O2”. X-ray diffraction, 4 ligands (BHR, FE, CL), 7 pockets (best druggability 0.88). MolNFT v1 #72135 on GenesisL1…
- PDB
- 3MZB
- Type
- protein
- Length
- 994 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nickel-binding periplasmic protein
- EC
- 3.6.3.24
- UniProt
- P33590
- Ligands
- BHR, FE, CL, SO4
- Pockets
- 7 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nickel-binding periplasmic protein (EC 3.6.3.24) | protein | 498 | 31% helix, 25% strand | P33590 |
| B | Nickel-binding periplasmic protein (EC 3.6.3.24) | protein | 496 | 31% helix, 25% strand | P33590 |
Ligands and binding sites
- BHR · 2-[2-[carboxymethyl-[(2-hydroxyphenyl)methyl]amino]ethyl-[(2,3-dihydroxyphenyl)methyl]amino]ethanoic acid · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 13 copies · chains A, B
- ACT · Acetate ion · additive · 11 copies · chains A, B
- DTD · Dithiane diol · additive · 2 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.88 | 0.90 | 147 | ACT, GOL |
| 2 | 1037 | 0.78 | 0.80 | 69 | ACT, CL, BHR, FE, DTD |
| 3 | 1118 | 0.77 | 0.79 | 67 | ACT, CL, BHR, FE, DTD |
| 4 | 132 | 0.72 | 0.91 | 29 | GOL |
| 5 | 161 | 0.72 | 0.90 | 30 | ACT |
Interfaces
1 interface between chains.
- A–B · 1655 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3MZB · X-ray structure of NikA in complex with the doubly hydroxylated iron complex, 1-O2 · 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 3MZB · PDBe 3MZB · UniProt P33590
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