7XL1
| Crystal structure of chimeric 7D12-Vob nanobody at 1.65 Angstrom | Descriptor: | Chimeric 7D12-Vob nanobody, MALONATE ION | Authors: | Caaveiro, J.M.M, Kinoshita, S, Mori, C, Nakakido, M, Tsumoto, K. | Deposit date: | 2022-04-20 | Release date: | 2022-11-09 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Molecular basis for thermal stability and affinity in a VHH: Contribution of the framework region and its influence in the conformation of the CDR3. Protein Sci., 31, 2022
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7XLI
| Crystal structure of IsdB linker-NEAT2 bound to a nanobody (VHH) | Descriptor: | CALCIUM ION, CHLORIDE ION, Iron-regulated surface determinant protein B, ... | Authors: | Caaveiro, J.M.M, Valenciano-Bellido, S, Tsumoto, K. | Deposit date: | 2022-04-21 | Release date: | 2023-05-31 | Last modified: | 2024-03-06 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Targeting hemoglobin receptors IsdH and IsdB of Staphylococcus aureus with a single VHH antibody inhibits bacterial growth. J.Biol.Chem., 299, 2023
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7CUE
| Crystal structure of HID2 bound to human Hemoglobin | Descriptor: | Amino acid ABC transporter substrate-binding protein, Hemoglobin subunit alpha, Hemoglobin subunit beta, ... | Authors: | Caaveiro, J.M.M, Hoshino, M, Tsumoto, K. | Deposit date: | 2020-08-22 | Release date: | 2021-07-07 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.75 Å) | Cite: | Structural basis for the recognition of human hemoglobin by the Shr protein from Streptococcus pyogenes To Be Published
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7CUD
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7EV1
| Crystal structure of LI-Cadherin EC1-2 | Descriptor: | ACETATE ION, CALCIUM ION, Cadherin-17, ... | Authors: | Caaveiro, J.M.M, Yui, A, Tsumoto, K. | Deposit date: | 2021-05-19 | Release date: | 2021-06-16 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.38 Å) | Cite: | Mechanism of dimerization and structural features of human LI-cadherin. J.Biol.Chem., 297, 2021
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7CYM
| Crystal structure of LI-Cadherin EC1-4 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, ... | Authors: | Caaveiro, J.M.M, Yui, A, Tsumoto, K. | Deposit date: | 2020-09-03 | Release date: | 2021-08-18 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.7 Å) | Cite: | Mechanism of dimerization and structural features of human LI-cadherin. J.Biol.Chem., 297, 2021
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7EKB
| Crystal structure of 4E10 modified with pyrene acetamide | Descriptor: | ACETATE ION, Fab region of the heavy chain of broadly neutralizing antibody anti-HIV-1 4E10, Fab region of the light chain of the broadly neutralizing anti-HIV-1 antibody 4E10, ... | Authors: | Caaveiro, J.M.M, Rujas, E, Nieva, J.L. | Deposit date: | 2021-04-05 | Release date: | 2021-08-11 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.45 Å) | Cite: | Focal accumulation of aromaticity at the CDRH3 loop mitigates 4E10 polyreactivity without altering its HIV neutralization profile. Iscience, 24, 2021
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7EKK
| Anti-HIV-1 broadly neutralizing antibody delta-loop 4E10 modified with pyrene acetamide | Descriptor: | AMMONIUM ION, CHLORIDE ION, GLYCEROL, ... | Authors: | Caaveiro, J.M.M, Rujas, E, Nieva, J.L. | Deposit date: | 2021-04-05 | Release date: | 2021-08-11 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Focal accumulation of aromaticity at the CDRH3 loop mitigates 4E10 polyreactivity without altering its HIV neutralization profile. Iscience, 24, 2021
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3CPO
| Crystal structure of ketosteroid isomerase D40N with bound 2-fluorophenol | Descriptor: | 2-fluorophenol, Delta(5)-3-ketosteroid isomerase | Authors: | Caaveiro, J.M.M, Pybus, B, Ringe, D, Petsko, G. | Deposit date: | 2008-03-31 | Release date: | 2008-09-23 | Last modified: | 2023-08-30 | Method: | X-RAY DIFFRACTION (1.24 Å) | Cite: | Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole J.Am.Chem.Soc., 130, 2008
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4ZMO
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4ZMY
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4ZMN
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4ZMX
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4ZMQ
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4ZMW
| Crystal structure of human P-cadherin (enc-X-dimer) | Descriptor: | CALCIUM ION, Cadherin-3, NICKEL (II) ION, ... | Authors: | Caaveiro, J.M.M, Kudo, S, Tsumoto, K. | Deposit date: | 2015-05-04 | Release date: | 2016-09-07 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Adhesive Dimerization of Human P-Cadherin Catalyzed by a Chaperone-like Mechanism Structure, 24, 2016
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4ZMT
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5BPG
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4ZML
| Crystal structure of human P-cadherin (ss-dimer) | Descriptor: | CALCIUM ION, CHLORIDE ION, Cadherin-3, ... | Authors: | Caaveiro, J.M.M, Kudo, S, Tsumoto, K. | Deposit date: | 2015-05-04 | Release date: | 2016-09-07 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Adhesive Dimerization of Human P-Cadherin Catalyzed by a Chaperone-like Mechanism Structure, 24, 2016
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4ZMV
| Crystal structure of human P-cadherin (ss-X-dimer pocket I) | Descriptor: | CALCIUM ION, Cadherin-3, GLYCEROL, ... | Authors: | Caaveiro, J.M.M, Kudo, S, Tsumoto, K. | Deposit date: | 2015-05-04 | Release date: | 2016-09-07 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Adhesive Dimerization of Human P-Cadherin Catalyzed by a Chaperone-like Mechanism Structure, 24, 2016
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4ZMP
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4ZMZ
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5BTQ
| Crystal structure of human heme oxygenase 1 H25R with biliverdin bound | Descriptor: | BILIVERDINE IX ALPHA, Heme oxygenase 1, SULFATE ION | Authors: | Caaveiro, J.M.M, Morante, K, Sigala, P, Tsumoto, K. | Deposit date: | 2015-06-03 | Release date: | 2016-06-08 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.08 Å) | Cite: | In-Cell Enzymology To Probe His-Heme Ligation in Heme Oxygenase Catalysis Biochemistry, 55, 2016
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5CIP
| Crystal Structure of Unbound 4E10 | Descriptor: | FAB 4E10 HEAVY CHAIN, FAB 4E10 LIGHT CHAIN | Authors: | Caaveiro, J.M.M, Rujas, E, Nieva, J.L, Tsumoto, K. | Deposit date: | 2015-07-13 | Release date: | 2015-09-23 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.48 Å) | Cite: | Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10 J.Virol., 89, 2015
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5CIL
| Crystal Structure of non-neutralizing version of 4E10 (WDWD) with epitope bound | Descriptor: | ACETATE ION, CHLORIDE ION, FAB 4E10 HEAVY CHAIN, ... | Authors: | Caaveiro, J.M.M, Rujas, E, Nieva, J.L, Tsumoto, K. | Deposit date: | 2015-07-13 | Release date: | 2015-09-23 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.81 Å) | Cite: | Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10 J.Virol., 89, 2015
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5CIN
| Crystal Structure of non-neutralizing version of 4E10 (DeltaLoop) with epitope bound | Descriptor: | CHLORIDE ION, FAB 4E10 HEAVY CHAIN, FAB 4E10 LIGHT CHAIN, ... | Authors: | Caaveiro, J.M.M, Rujas, E, Nieva, J.L, Tsumoto, K. | Deposit date: | 2015-07-13 | Release date: | 2015-09-23 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10 J.Virol., 89, 2015
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