MolNFT v1 · #61560 · protein
Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter nika (nickel butane-1,2,4- tricarboxylate form)
3DP8 · Nickel-binding periplasmic protein: “Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter…”. X-ray diffraction, 4 ligands (HCT, NI, CL), 11 pockets (best druggability 0.87).…
- PDB
- 3DP8
- Type
- protein
- Length
- 1,491 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nickel-binding periplasmic protein
- UniProt
- P33590
- Ligands
- HCT, NI, CL, SO4
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 23% 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, 23% strand | P33590 |
| C | Nickel-binding periplasmic protein | protein | 496 | 30% helix, 22% strand | P33590 |
Ligands and binding sites
- HCT · (2R)-butane-1,2,4-tricarboxylic acid · ligand · 3 copies · chains A, B, C
- NI · Nickel (II) ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 7 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains A
- ACT · Acetate ion · additive · 11 copies · chains A, B, C
- GOL · Glycerol · additive · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.87 | 0.88 | 165 | ACT, CL |
| 2 | 516 | 0.85 | 0.91 | 54 | NI, HCT |
| 3 | 533 | 0.85 | 0.91 | 63 | NI, ACT, HCT |
| 4 | 1143 | 0.78 | 0.80 | 68 | NI, ACT, CL, HCT |
| 5 | 516 | 0.67 | 0.78 | 64 | GOL, CL |
Interfaces
2 interfaces between chains.
- A–B · 1360 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 720 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3DP8 · Structural characterization of a putative endogenous metal chelator in the periplasmic… · 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 0.88
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 3DP8 · PDBe 3DP8 · UniProt P33590
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