MolNFT v1 · #24051 · protein
Crystal structures of the liganded and unliganded nickel binding protein nika from escherichia COLI (nickel liganded form)
1UIV · Nickel-binding periplasmic protein: “Crystal structures of the liganded and unliganded nickel binding protein nika from escherichia COLI (nickel…”. X-ray diffraction, 1 ligand (NI), 7 pockets (best druggability 0.89). MolNFT v1…
- 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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