5N5J
 
 | | Human MMP12 in complex with 3-(5-(1,2-dithiolan-3-yl)pentanamido)propane-1-sulfonate | | Descriptor: | 3-[5-[(3~{S})-1,2-dithiolan-3-yl]pentanoylamino]propane-1-sulfonic acid, ACETOHYDROXAMIC ACID, CALCIUM ION, ... | | Authors: | Calderone, V. | | Deposit date: | 2017-02-14 | | Release date: | 2017-11-01 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Lipoyl-Homotaurine Derivative (ADM_12) Reverts Oxaliplatin-Induced Neuropathy and Reduces Cancer Cells Malignancy by Inhibiting Carbonic Anhydrase IX (CAIX).
J. Med. Chem., 60, 2017
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5HYD
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2B8J
 | | Crystal structure of AphA class B acid phosphatase/phosphotransferase ternary complex with adenosine and phosphate at 2 A resolution | | Descriptor: | ADENOSINE, GOLD 3+ ION, GOLD ION, ... | | Authors: | Calderone, V, Forleo, C, Benvenuti, M, Thaller, M.C, Rossolini, G.M, Mangani, S. | | Deposit date: | 2005-10-07 | | Release date: | 2005-11-29 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (2.033 Å) | | Cite: | A structure-based proposal for the catalytic mechanism of the bacterial acid phosphatase AphA belonging to the DDDD superfamily of phosphohydrolases
J.Mol.Biol., 355, 2006
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2B82
 | | Crystal structure of AphA class B acid phosphatase/phosphotransferase ternary complex with adenosine and phosphate bound to the catalytic metal at 1.2 A resolution | | Descriptor: | ADENOSINE, MAGNESIUM ION, PHOSPHATE ION, ... | | Authors: | Calderone, V, Forleo, C, Benvenuti, M, Thaller, M.C, Rossolini, G.M, Mangani, S. | | Deposit date: | 2005-10-06 | | Release date: | 2005-11-29 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (1.25 Å) | | Cite: | A structure-based proposal for the catalytic mechanism of the bacterial acid phosphatase AphA belonging to the DDDD superfamily of phosphohydrolases
J.Mol.Biol., 355, 2006
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7A70
 | | HEW lysozyme in complex with Ti(OH)4 | | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, Lysozyme, ... | | Authors: | Calderone, V, Gigli, L, Ravera, E, Luchinat, C. | | Deposit date: | 2020-08-27 | | Release date: | 2021-01-13 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | On the Mechanism of Bioinspired Formation of Inorganic Oxides: Structural Evidence of the Electrostatic Nature of the Interaction between a Mononuclear Inorganic Precursor and Lysozyme.
Biomolecules, 11, 2020
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6H6S
 | | Sad phasing on nickel-substituted human carbonic anhydrase II | | Descriptor: | Carbonic anhydrase 2, NICKEL (II) ION | | Authors: | Calderone, V, Fragai, M, Silva, J.P, Luchinat, C, Ravera, E, Geraldes, C.F.G.C, Macedo, A.L, Cerofolini, L, Giuntini, S. | | Deposit date: | 2018-07-30 | | Release date: | 2019-01-09 | | Last modified: | 2024-05-15 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Non-crystallographic symmetry in proteins: Jahn-Teller-like and Butterfly-like effects?
J. Biol. Inorg. Chem., 24, 2019
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6GEU
 | | Crystal structure of the C230A mutant of human IBA57 | | Descriptor: | Putative transferase CAF17, mitochondrial | | Authors: | Calderone, V, Ciofi-Baffoni, S, Gourdoupis, S, Banci, L, Nasta, V. | | Deposit date: | 2018-04-27 | | Release date: | 2019-04-03 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | IBA57 Recruits ISCA2 to Form a [2Fe-2S] Cluster-Mediated Complex.
J.Am.Chem.Soc., 140, 2018
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6QE4
 | | Re-refinement of 5OLI human IBA57-I3C | | Descriptor: | 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid, Putative transferase CAF17, mitochondrial | | Authors: | Calderone, V, Ciofi-Baffoni, S, Gourdoupis, S, Banci, L, Nasta, V. | | Deposit date: | 2019-01-04 | | Release date: | 2019-03-13 | | Last modified: | 2024-05-15 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | In-house high-energy-remote SAD phasing using the magic triangle: how to tackle the P1 low symmetry using multiple orientations of the same crystal of human IBA57 to increase the multiplicity.
Acta Crystallogr D Struct Biol, 75, 2019
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6QE3
 | | Re-refinement of 6ESR human IBA57 at 1.75 A resolution | | Descriptor: | Putative transferase CAF17, mitochondrial | | Authors: | Calderone, V, Ciofi-Baffoni, S, Gourdoupis, S, Banci, L. | | Deposit date: | 2019-01-04 | | Release date: | 2019-03-13 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | In-house high-energy-remote SAD phasing using the magic triangle: how to tackle the P1 low symmetry using multiple orientations of the same crystal of human IBA57 to increase the multiplicity.
Acta Crystallogr D Struct Biol, 75, 2019
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7NWX
 | | SARS-COV2 NSP5 in the presence of Zn2+ | | Descriptor: | Replicase polyprotein 1a, ZINC ION | | Authors: | Calderone, V, Grifagni, D, Cantini, F, Fragai, M, Banci, L. | | Deposit date: | 2021-03-17 | | Release date: | 2022-01-26 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | SARS-CoV-2 M pro inhibition by a zinc ion: structural features and hints for drug design.
Chem.Commun.(Camb.), 57, 2021
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7NXH
 | | Structure of SARS-CoV2 NSP5 (3C-like proteinase) determined in-house | | Descriptor: | 3C-like proteinase | | Authors: | Calderone, V, Grifagni, D, Cantini, F, Fragai, M, Banci, L. | | Deposit date: | 2021-03-18 | | Release date: | 2022-01-26 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | SARS-CoV-2 M pro inhibition by a zinc ion: structural features and hints for drug design.
Chem.Commun.(Camb.), 57, 2021
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8OKB
 | | SARS-CoV2 NSP5 in complex with a peptidomimetic ligand | | Descriptor: | 3C-like proteinase nsp5, methyl (4~{S})-4-[[(2~{S})-4-methyl-2-(phenylmethoxycarbonylamino)pentanoyl]amino]-5-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]pentanoate | | Authors: | Calderone, V. | | Deposit date: | 2023-03-28 | | Release date: | 2024-01-17 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (2.31 Å) | | Cite: | Development of a GC-376 Based Peptidomimetic PROTAC as a Degrader of 3-Chymotrypsin-like Protease of SARS-CoV-2.
Acs Med.Chem.Lett., 15, 2024
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8OKC
 | | SARS-CoV2 NSP5 in complex with a GC-376 based peptidomimetic PROTAC | | Descriptor: | (phenylmethyl) ~{N}-[(2~{R})-1-[[(~{Z},2~{S})-5-[4-[[1-[2-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1,3-bis(oxidanylidene)isoindol-5-yl]piperidin-4-yl]methyl]piperazin-1-yl]-5-oxidanylidene-1-[(3~{R})-2-oxidanylidenepyrrolidin-3-yl]pent-3-en-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate, 3C-like proteinase nsp5 | | Authors: | Calderone, V. | | Deposit date: | 2023-03-28 | | Release date: | 2024-01-17 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Development of a GC-376 Based Peptidomimetic PROTAC as a Degrader of 3-Chymotrypsin-like Protease of SARS-CoV-2.
Acs Med.Chem.Lett., 15, 2024
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1XTL
 | | Crystal structure of P104H mutant of SOD-like protein from Bacillus subtilis. | | Descriptor: | COPPER (II) ION, Hypothetical superoxide dismutase-like protein yojM, ZINC ION | | Authors: | Calderone, V, Mangani, S, Banci, L, Benvenuti, M, Bertini, I, Viezzoli, M.S, Fantoni, A. | | Deposit date: | 2004-10-22 | | Release date: | 2005-10-04 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | From an Inactive Prokaryotic SOD Homologue to an Active Protein through Site-Directed Mutagenesis.
J.Am.Chem.Soc., 127, 2005
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5N5K
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6RLY
 | | Human MMP12 (catalytic domain) in complex with AP316 | | Descriptor: | 2-(3-oxidanyl-2-oxidanylidene-pyridin-1-yl)-~{N}-[2-(4-phenylphenyl)ethyl]ethanamide, ACETOHYDROXAMIC ACID, CALCIUM ION, ... | | Authors: | Calderone, V, Fragai, M, Luchinat, C. | | Deposit date: | 2019-05-03 | | Release date: | 2020-03-11 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Exploration of zinc-binding groups for the design of inhibitors for the oxytocinase subfamily of M1 aminopeptidases.
Bioorg.Med.Chem., 27, 2019
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6RD0
 | | Human MMP12 catalytic domain in complex with AP280 | | Descriptor: | ACETOHYDROXAMIC ACID, CALCIUM ION, Macrophage metalloelastase, ... | | Authors: | Calderone, V, Fragai, M, Luchinat, C. | | Deposit date: | 2019-04-12 | | Release date: | 2020-02-19 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Exploration of zinc-binding groups for the design of inhibitors for the oxytocinase subfamily of M1 aminopeptidases.
Bioorg.Med.Chem., 27, 2019
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1XTM
 | | Crystal structure of the double mutant Y88H-P104H of a SOD-like protein from Bacillus subtilis. | | Descriptor: | COPPER (II) ION, Hypothetical superoxide dismutase-like protein yojM, ZINC ION | | Authors: | Calderone, V, Mangani, S, Banci, L, Benvenuti, M, Bertini, I, Fantoni, A, Viezzoli, M.S. | | Deposit date: | 2004-10-22 | | Release date: | 2005-10-04 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | From an Inactive Prokaryotic SOD Homologue to an Active Protein through Site-Directed Mutagenesis.
J.Am.Chem.Soc., 127, 2005
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1GGL
 | | HUMAN CELLULAR RETINOL BINDING PROTEIN III | | Descriptor: | PROTEIN (CELLULAR RETINOL-BINDING PROTEIN III) | | Authors: | Calderone, V, Zanotti, G, Folli, C, Ottonello, S, Bolchi, A, Stoppini, M, Berni, R. | | Deposit date: | 2000-08-23 | | Release date: | 2001-03-07 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (2.31 Å) | | Cite: | Identification, retinoid binding, and x-ray analysis of a human retinol-binding protein.
Proc.Natl.Acad.Sci.USA, 98, 2001
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6FFK
 | | Human apo-SOD1 bound to PtCl2(1R,2R-1,4-DACH | | Descriptor: | PtCl2(1(R),2(R)-DACH), Superoxide dismutase [Cu-Zn] | | Authors: | Calderone, V, Nativi, C, Cantini, F, Di Cesare Mannelli, L. | | Deposit date: | 2018-01-08 | | Release date: | 2018-11-28 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (1.94 Å) | | Cite: | Interaction of Half Oxa-/Halfcis-Platin Complex with Human Superoxide Dismutase and Induced Reduction of Neurotoxicity.
ACS Med Chem Lett, 9, 2018
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1RJU
 | | Crystal structure of a truncated form of yeast copper thionein | | Descriptor: | COPPER (I) ION, Metallothionein | | Authors: | Calderone, V, Dolderer, B, Hartmann, H.J, Echner, H, Luchinat, C, Del Bianco, C, Mangani, S, Weser, U. | | Deposit date: | 2003-11-20 | | Release date: | 2004-12-07 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (1.44 Å) | | Cite: | The Crystal Structure of Yeast Copper Thionein: the solution of a long lasting Enigma.
Proc.Natl.Acad.Sci.USA, 102, 2005
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1LPJ
 | | Human cRBP IV | | Descriptor: | Retinol-binding protein IV, cellular | | Authors: | Calderone, V, Zanotti, G, Berni, R, Folli, C. | | Deposit date: | 2002-05-08 | | Release date: | 2003-01-14 | | Last modified: | 2023-08-16 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Ligand binding and structural analysis of a human putative cellular retinol-binding protein
J.Biol.Chem., 277, 2002
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3N2U
 | | Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor N-hydroxy-2-(4-methoxy-N(2-(3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yloxy)ethyl)phenylsulfonamido)acetamide | | Descriptor: | CALCIUM ION, Macrophage metalloelastase, N-hydroxy-2-{[(4-methoxyphenyl)sulfonyl](2-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}ethyl)amino}acetamide, ... | | Authors: | Calderone, V. | | Deposit date: | 2010-05-19 | | Release date: | 2010-11-10 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.81 Å) | | Cite: | Structure-based approach to nanomolar, water soluble matrix metalloproteinases inhibitors (MMPIs).
Eur.J.Med.Chem., 45, 2010
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1RMT
 | | Crystal structure of AphA class B acid phosphatase/phosphotransferase complexed with adenosine. | | Descriptor: | ADENOSINE, Class B acid phosphatase, MAGNESIUM ION | | Authors: | Calderone, V, Forleo, C, Benvenuti, M, Rossolini, G.M, Thaller, M.C, Mangani, S. | | Deposit date: | 2003-11-28 | | Release date: | 2004-12-14 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Insights in the catalytic mechanism of AphA from Escherichia coli
To be Published
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2OXU
 | | Uninhibited form of human MMP-12 | | Descriptor: | CALCIUM ION, Macrophage metalloelastase, ZINC ION | | Authors: | Calderone, V, Bertini, I, Fragai, M, Luchinat, C, Maletta, M, Yeo, K.J. | | Deposit date: | 2007-02-21 | | Release date: | 2007-03-06 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (1.24 Å) | | Cite: | Snapshots of the reaction mechanism of matrix metalloproteinases.
ANGEW.CHEM.INT.ED.ENGL., 45, 2006
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