UniProt P33590
Nickel-binding periplasmic protein (P33590)
Nickel-binding periplasmic protein (UniProt P33590): 55 experimental structures and 1 predicted model on GenesisL1, 9 ligands bound, 18 pockets. Binding sites, druggability and experiment against prediction (TM-score) in GL1X.
- UniProt
- P33590
- Protein
- Nickel-binding periplasmic protein
- Experimental structures
- 55
- Predicted models
- 1
- Ligands
- 9
- Pockets
- 18 · 3 records with a druggable one
Structures
56 records of P33590 in the MolNFT archive: 55 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 1UIU | Crystal structures of the liganded and unliganded nickel binding protein NikA from Escherichia coli… | x-ray diffraction | A, B | — | — |
| 1UIU | Crystal structures of the liganded and unliganded nickel binding protein nika from escherichia COLI… | x-ray diffraction | A, B | — | — |
| 1UIV | Crystal structures of the liganded and unliganded nickel binding protein NikA from Escherichia coli… | x-ray diffraction | A, B | — | — |
| 1UIV | Crystal structures of the liganded and unliganded nickel binding protein nika from escherichia COLI… | x-ray diffraction | A, B | — | — |
| 1ZLQ | Crystallographic and spectroscopic evidence for high affinity binding of Fe EDTA (H2O)- to the… | x-ray diffraction | A, B | — | — |
| 1ZLQ | Crystallographic and spectroscopic evidence for high affinity binding of fe edta (H2O)- to the… | x-ray diffraction | A, B | — | — |
| 2NOO | Crystal Structure of Mutant NikA | x-ray diffraction | A | — | — |
| 2NOO | Crystal structure of mutant nika | x-ray diffraction | A | — | — |
| 3DP8 | Structural characterization of a putative endogenous metal chelator in the periplasmic nickel… | x-ray diffraction | A, B, C | — | — |
| 3DP8 | Structural characterization of a putative endogenous metal chelator in the periplasmic nickel… | x-ray diffraction | A, B, C | — | — |
| 3E3K | Structural characterization of a putative endogenous metal chelator in the periplasmic nickel… | x-ray diffraction | A, B, C | — | — |
| 3E3K | Structural characterization of a putative endogenous metal chelator in the periplasmic nickel… | x-ray diffraction | A, B, C | — | — |
| 3MVW | X-ray structure of a NikA+Iron complex" hybrid | x-ray diffraction | A, B | — | — |
| 3MVW | X-ray structure of a "NIKA+IRON complex" hybrid, NIKA/1 | x-ray diffraction | A, B | — | — |
| 3MVX | X-ray structure of the reduced NikA/1 hybrid, NikA/1-Red | x-ray diffraction | A, B | — | — |
| 3MVX | X-ray structure of the reduced NIKA/1 hybrid, NIKA/1-red | x-ray diffraction | A, B | — | — |
| 3MVY | X-ray structure of the diatomic oxo-intermediate NikA/1-Int', prior hydroxylation | x-ray diffraction | A, B | — | — |
| 3MVY | X-ray structure of the diatomic oxo-intermediate NIKA/1-int', prior hydroxylation | x-ray diffraction | A, B | — | — |
| 3MVZ | X-ray structure of the (hydro)peroxo intermediate NikA/1-Int | x-ray diffraction | A, B | — | — |
| 3MVZ | X-ray structure of the (HYDRO)PEROXO intermediate NIKA/1-int", after monohydroxylation of the iron… | x-ray diffraction | A, B | — | — |
| 3MW0 | X-ray structure of the doubly hydroxylated iron complex-NikA species, NikA1/O2 | x-ray diffraction | A, B | — | — |
| 3MW0 | X-ray structure of the doubly hydroxylated iron complex-nika species, NIKA1/O2 | x-ray diffraction | A, B | — | — |
| 3MZ9 | X-ray structure of NikA in complex with HBED | x-ray diffraction | A, B | — | — |
| 3MZ9 | X-ray structure of nika in complex with hbed | x-ray diffraction | A, B | — | — |
| 3MZB | X-ray structure of NikA in complex with the doubly hydroxylated iron complex, 1-O2 | x-ray diffraction | A, B | — | — |
| 3MZB | X-ray structure of nika in complex with the doubly hydroxylated iron complex, 1-O2 | x-ray diffraction | A, B | — | — |
| 3QIM | Histidine 416 of the periplamsic binding protein NikA is essential for nickel uptake in Escherichia… | x-ray diffraction | A, B | — | — |
| 3QIM | Histidine 416 of the periplamsic binding protein nika is essential for nickel uptake in escherichia… | x-ray diffraction | A, B | — | — |
| 4DCX | X-ray structure of NikA in complex with Fe(1R,2R)-N,N'-Bis(2-pyridylmethyl)-N,N'-dicarboxymethyl-1,2… | x-ray diffraction | A, B | — | — |
| 4DCX | X-ray structure of nika in complex with FE(1R,2R)-N,N'-BIS(2… | x-ray diffraction | A, B | — | — |
| 4DCY | X-ray structure of NikA in complex with Fe(1S,2S)-N,N-kappa-Bis(2-pyridylmethyl)-N-carboxymethyl-N-k… | x-ray diffraction | A, B | — | — |
| 4DCY | X-ray structure of nika in complex with FE(1S,2S)-N,N-kappa-BIS(2… | x-ray diffraction | A, B | — | — |
| 4I8C | X-ray structure of NikA in complex with Ni-(L-His)2 | x-ray diffraction | A, B, C | — | — |
| 4I8C | X-ray structure of nika in complex with ni-(L-HIS)2 | x-ray diffraction | A, B, C | — | — |
| 4I9D | X-ray structure of NikA in complex with Fe-N,N'-Bis(2-pyridylmethyl)-N-carboxymethyl-N'-methyl | x-ray diffraction | A, B | — | — |
| 4I9D | X-ray structure of nika in complex with fe-N,N'-BIS(2-pyridylmethyl)- N-carboxymethyl-N'-methyl | x-ray diffraction | A, B | — | — |
| 5L8D | X-ray structure of NikA from Escherichia coli in complex with Ru(bis(pyrzol-1-yl)acetate… | x-ray diffraction | A, B | SO4, FE, EDT, RU, CL, 6RP | 7 (best 0.89) |
| 5L8D | X-ray structure of nika from escherichia COLI in complex with RU(BIS(PYRZOL-1-YL)ACETATE… | x-ray diffraction | A, B | SO4, EDT, RU, CL, CMO | — |
| 5MWU | Crystal structure of the periplasmic nickel-binding protein NikA from Escherichia coli in complex… | x-ray diffraction | A, B | SO4, EDT, RU, CL, CMO | — |
| 5MWU | Crystal structure of the periplasmic nickel-binding protein nika from escherichia COLI in complex… | x-ray diffraction | A, B | SO4, EDT, RU, CL, CMO | — |
| 5ON0 | Crystal structure of NikA in complex with Fe-L2 (N-(2-hydroxy-3methoxybenzyl)-N-N'-ethylenediaminedi… | x-ray diffraction | A, B | FE, SO4, CL | — |
| 5ON0 | Crystal structure of nika in complex with fe-L2 (N-(2-hydroxy… | x-ray diffraction | A, B | FE, SO4, CL | — |
| 5ON1 | Crystal structure of NikA in complex with hydroxylated Fe-L1… | x-ray diffraction | A, B | FE, SO4, CL | — |
| 5ON1 | Crystal structure of nika in complex with hydroxylated fe-L1 (N-(2… | x-ray diffraction | A, B | FE, SO4, CL | — |
| 5ON4 | Crystal structure of NikA in complex with Fe-L1 (N-(2-hydroxybenzyl)-N'-(2-thiomethylbenzyl)-N,N'-et… | x-ray diffraction | A, B | FE | — |
| 5ON4 | Crystal structure of nika in complex with fe-L1 (N-(2-hydroxybenzyl)… | x-ray diffraction | A, B | FE | — |
| 5ON5 | Crystal structure of NikA in complex with Fe-L2 (Fe-L2… | x-ray diffraction | A, B | FE, CL | — |
| 5ON5 | Crystal structure of nika in complex with fe-L2 (fe-L2 (N-(2-hydroxy… | x-ray diffraction | A, B | FE, CL | — |
| 5ON8 | Crystal structure of NikA in complex with reduced Fe-L2… | x-ray diffraction | A, B | FE, SO4, CL | — |
| 5ON8 | Crystal structure of nika in complex with reduced fe-L2 (N-(2-hydroxy… | x-ray diffraction | A, B | FE, SO4, CL | — |
| 5ON9 | Crystal structure of NikA in complex with reduced Fe-L1… | x-ray diffraction | A, B | FE, CL | — |
| 5ON9 | Crystal structure of nika in complex with reduced fe-L1 (N-(2… | x-ray diffraction | A, B | FE, CL | — |
| 6R4Q | Crystal structure of the periplasmic nickel-binding protein nika from escherichia COLI in complex… | x-ray diffraction | A, B | EDT, CL, RU, CMO | — |
| 7A0C | X-ray structure of NikA from Escherichia coli in complex with Fe-6-Me2-BPMCN | x-ray diffraction | A, B | FE, QTT, MG, CL | 6 (best 0.86) |
| 7A0C | X-ray structure of nika from escherichia COLI in complex with fe-6- ME2-bpmcn | x-ray diffraction | A, B | QTT, MG, CL | — |
| P33590 | AlphaFold monomer V2.0 prediction for nickel-binding periplasmic protein (P33590) | predicted | A | — | 5 (best 0.67) |
Ligands
- CL · Chloride ion · in 17 records
- FE · Fe (III) ion · in 14 records
- SO4 · Sulfate ion · in 10 records
- CMO · Carbon monoxide · in 5 records
- EDT · {[-(bis-carboxymethyl-amino)-ethyl]-carboxymethyl-amino}-acetic acid · in 5 records
- RU · Ruthenium ion · in 5 records
- MG · Magnesium ion · in 2 records
- QTT · 2-[[(1~{S},2~{S})-2-[methyl-[(6-methylpyridin-2-yl) methyl]amino]cyclohexyl]-[(6-methylpyridin-2-yl) methyl]amino]ethanoic acid · in 2 records
- 6RP · bis(pyrzol-1-yl)acetate scorpionate · in 1 record
Experiment against prediction
- 1UIU chain A against the predicted model P33590: TM-score 0.99, RMSD 0.68 Å
- 1UIU chain A against the predicted model P33590: TM-score 0.99, RMSD 0.68 Å
- 2NOO chain A against the predicted model P33590: TM-score 0.97, RMSD 1.51 Å
- 2NOO chain A against the predicted model P33590: TM-score 0.97, RMSD 1.51 Å
- 4DCY chain A against the predicted model P33590: TM-score 0.95, RMSD 1.87 Å
- 4DCY chain A against the predicted model P33590: TM-score 0.95, RMSD 1.87 Å
- 3MVY chain A against the predicted model P33590: TM-score 0.94, RMSD 2.00 Å
- 3MVY chain A against the predicted model P33590: TM-score 0.94, RMSD 2.00 Å
- 4I9D chain A against the predicted model P33590: TM-score 0.94, RMSD 1.94 Å
- 4I9D chain A against the predicted model P33590: TM-score 0.94, RMSD 1.94 Å
Elsewhere
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