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Crystal structures of the liganded and unliganded nickel binding protein nika from escherichia COLI (nickel liganded form)
Analyse Crystal structures of the liganded and unliganded nickel binding protein nika… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UIV
- Type
- protein
- Length
- 993 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nickel-binding periplasmic protein
- UniProt
- P33590
- Ligands
- NI
- Pockets
- 7 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nickel-binding periplasmic protein | protein | 497 | 31% helix, 23% strand | P33590 |
| B | Nickel-binding periplasmic protein | protein | 496 | 31% helix, 24% strand | P33590 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A
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 | 955 | 0.89 | 0.90 | 131 | empty |
| 2 | 1092 | 0.80 | 0.81 | 71 | NI |
| 3 | 1181 | 0.77 | 0.79 | 69 | NI |
| 4 | 131 | 0.70 | 0.91 | 27 | empty |
| 5 | 149 | 0.70 | 0.90 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1522 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 1UIV · Crystal structures of the liganded and unliganded nickel binding protein NikA from… · 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 B 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 1UIV · PDBe 1UIV · UniProt P33590
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