Research workbench
Crystal structure of the periplasmic nickel-binding protein nika from escherichia COLI in complex with RU(BPZA)CO H2O cl
Analyse Crystal structure of the periplasmic nickel-binding protein nika from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R4Q
- Type
- protein
- Length
- 995 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nickel-binding periplasmic protein
- UniProt
- P33590
- Ligands
- EDT, 6RP, FE, RU, CL, CMO
- 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 | 31% helix, 23% strand | P33590 |
| B | Nickel-binding periplasmic protein | protein | 497 | 31% helix, 25% strand | P33590 |
Ligands and binding sites
- EDT · {[-(bis-carboxymethyl-amino)-ethyl]-carboxymethyl-amino}-acetic acid · ligand · chains A
- 6RP · bis(pyrzol-1-yl)acetate scorpionate · ligand · chains B
- FE · Fe (III) ion · metal · chains A
- RU · Ruthenium ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
- CMO · Carbon monoxide · ion · chains B
- GOL · Glycerol · additive · 19 copies · chains A, B
- ACT · Acetate ion · 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 | 1095 | 0.89 | 0.90 | 154 | GOL |
| 2 | 1196 | 0.77 | 0.79 | 74 | FE, EDT, CL, GOL, ACT |
| 3 | 1195 | 0.77 | 0.79 | 69 | RU, 6RP, CL, CMO, GOL |
| 4 | 318 | 0.71 | 0.84 | 41 | empty |
| 5 | 81 | 0.65 | 0.91 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1558 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6R4Q · Crystal structure of the periplasmic nickel-binding protein NikA from Escherichia coli 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 6R4Q · PDBe 6R4Q · UniProt P33590
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