5GWF
| FraC with GlcNAc(6S) bound | Descriptor: | 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose, CHLORIDE ION, DELTA-actitoxin-Afr1a, ... | Authors: | Caaveiro, J.M.M, Tsumoto, K. | Deposit date: | 2016-09-11 | Release date: | 2017-06-21 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.55 Å) | Cite: | Haemolytic actinoporins interact with carbohydrates using their lipid-binding module Philos. Trans. R. Soc. Lond., B, Biol. Sci., 372, 2017
|
|
6K2G
| |
1UFU
| Crystal structure of ligand binding domain of immunoglobulin-like transcript 2 (ILT2; LIR-1) | Descriptor: | Immunoglobulin-like transcript 2 | Authors: | Shiroishi, M, Amano, K, Rasubala, L, Tsumoto, K, Kumagai, I, Kohda, D, Maenaka, K. | Deposit date: | 2003-06-10 | Release date: | 2004-08-10 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (3 Å) | Cite: | Kinetic and thermodynamic properties of the interaction between Immunoglobulin like transcript (ILT) and MHC class I To be Published
|
|
6JB2
| Crystal structure of nanobody D3-L11 mutant Y102A in complex with hen egg-white lysozyme | Descriptor: | CHLORIDE ION, GLYCEROL, Lysozyme C, ... | Authors: | Caaveiro, J.M.M, Tamura, H, Akiba, H, Tsumoto, K. | Deposit date: | 2019-01-25 | Release date: | 2019-11-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody. Sci Rep, 9, 2019
|
|
6JB9
| Crystal structure of nanobody D3-L11 (unbound form) | Descriptor: | Nanobody D3-L11, SULFATE ION | Authors: | Caaveiro, J.M.M, Tamura, H, Akiba, H, Tsumoto, K. | Deposit date: | 2019-01-25 | Release date: | 2019-11-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.15 Å) | Cite: | Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody. Sci Rep, 9, 2019
|
|
6JB8
| Crystal structure of nanobody D3-L11 in complex with hen egg-white lysozyme | Descriptor: | CHLORIDE ION, GLYCEROL, Lysozyme C, ... | Authors: | Caaveiro, J.M.M, Tamura, H, Akiba, H, Tsumoto, K. | Deposit date: | 2019-01-25 | Release date: | 2019-11-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody. Sci Rep, 9, 2019
|
|
6JB5
| Crystal structure of nanobody D3-L11 mutant Y102A in complex with hen egg-white lysozyme (form II) | Descriptor: | CHLORIDE ION, GLYCEROL, Lysozyme C, ... | Authors: | Caaveiro, J.M.M, Tamura, H, Akiba, H, Tsumoto, K. | Deposit date: | 2019-01-25 | Release date: | 2019-11-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.55 Å) | Cite: | Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody. Sci Rep, 9, 2019
|
|
1WT5
| The Crystal Structure Of A Humanized Antibody Fv 528 | Descriptor: | ANTI EGFR ANTIBODY FV REGION | Authors: | Makabe, K, Tsumoto, K, Asano, R, Kondo, H, Kumagai, I. | Deposit date: | 2004-11-16 | Release date: | 2005-05-16 | Last modified: | 2011-07-13 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Thermodynamic consequences of mutations in vernier zone residues of a humanized anti-human epidermal growth factor receptor murine antibody, 528 J.Biol.Chem., 283, 2008
|
|
7XL0
| Crystal structure of Vobarilizumab at 1.70 Angstrom | Descriptor: | GLYCEROL, Nanobody Vobarilizumab, SULFATE ION | Authors: | Caaveiro, J.M.M, Mori, C, Kinoshita, S, Nakakido, M, Tsumoto, K. | Deposit date: | 2022-04-20 | Release date: | 2022-11-09 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.7 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
|
|
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
|
|
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
|
|
7XLD
| Crystal structure of IsdH linker-NEAT3 bound to a nanobody (VHH) | Descriptor: | Iron-regulated surface determinant protein H, MAGNESIUM ION, Nanobody VHH6, ... | Authors: | Caaveiro, J.M.M, Valenciano-Bellido, S, Tsumoto, K. | Deposit date: | 2022-04-21 | Release date: | 2023-05-31 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.65 Å) | Cite: | Targeting hemoglobin receptors IsdH and IsdB of Staphylococcus aureus with a single VHH antibody inhibits bacterial growth. J.Biol.Chem., 299, 2023
|
|
5GHW
| Crystal structure of broad neutralizing antibody 10E8 with long epitope bound | Descriptor: | Endogenous retrovirus group K member 8 Env polyprotein, FAB 10E8 HEAVY CHAIN, FAB 10E8 LIGHT CHAIN, ... | Authors: | Caaveiro, J.M.M, Rujas, E, Morante, K, Nieva, J.L, Tsumoto, K. | Deposit date: | 2016-06-21 | Release date: | 2016-11-23 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Structural basis for broad neutralization of HIV-1 through the molecular recognition of 10E8 helical epitope at the membrane interface Sci Rep, 6, 2016
|
|
4TSO
| Crystal structure of FraC with DHPC bound (crystal form I) | Descriptor: | 1,2-dihexanoyl-sn-glycero-3-phosphocholine, Fragaceatoxin C, PHOSPHATE ION, ... | Authors: | Caaveiro, J.M.M, Tanaka, K, Tsumoto, K. | Deposit date: | 2014-06-19 | Release date: | 2015-03-04 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structural basis for self-assembly of a cytolytic pore lined by protein and lipid Nat Commun, 6, 2015
|
|
4TSP
| Crystal structure of FraC with DHPC bound (crystal form II) | Descriptor: | 1,2-dihexanoyl-sn-glycero-3-phosphocholine, Fragaceatoxin C, PHOSPHATE ION, ... | Authors: | Caaveiro, J.M.M, Tanaka, K, Tsumoto, K. | Deposit date: | 2014-06-19 | Release date: | 2015-03-04 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.15 Å) | Cite: | Structural basis for self-assembly of a cytolytic pore lined by protein and lipid Nat Commun, 6, 2015
|
|
4TSY
| Crystal structure of FraC with lipids | Descriptor: | 2-[[(E,2S,3R)-2-(hexanoylamino)-3-oxidanyl-dec-4-enoxy]-oxidanyl-phosphoryl]oxyethyl-trimethyl-azanium, Fragaceatoxin C, HEPTANE-1,2,3-TRIOL, ... | Authors: | Caaveiro, J.M.M, Tanaka, K, Tsumoto, K. | Deposit date: | 2014-06-19 | Release date: | 2015-03-04 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (3.14 Å) | Cite: | Structural basis for self-assembly of a cytolytic pore lined by protein and lipid Nat Commun, 6, 2015
|
|
4TSL
| Crystal structure of FraC with POC bound (crystal form I) | Descriptor: | ACETATE ION, FORMIC ACID, Fragaceatoxin C, ... | Authors: | Caaveiro, J.M.M, Tanaka, K, Tsumoto, K. | Deposit date: | 2014-06-19 | Release date: | 2015-03-04 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Structural basis for self-assembly of a cytolytic pore lined by protein and lipid Nat Commun, 6, 2015
|
|
4TSN
| Crystal structure of FraC with POC bound (crystal form II) | Descriptor: | ACETATE ION, Fragaceatoxin C, GLYCEROL, ... | Authors: | Caaveiro, J.M.M, Tanaka, K, Tsumoto, K. | Deposit date: | 2014-06-19 | Release date: | 2015-03-04 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.57 Å) | Cite: | Structural basis for self-assembly of a cytolytic pore lined by protein and lipid Nat Commun, 6, 2015
|
|
4TSQ
| Crystal structure of FraC with DHPC bound (crystal form III) | Descriptor: | 1,2-dihexanoyl-sn-glycero-3-phosphocholine, CHLORIDE ION, Fragaceatoxin C, ... | Authors: | Caaveiro, J.M.M, Tanaka, K, Tsumoto, K. | Deposit date: | 2014-06-19 | Release date: | 2015-03-04 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Structural basis for self-assembly of a cytolytic pore lined by protein and lipid Nat Commun, 6, 2015
|
|
1HMK
| RECOMBINANT GOAT ALPHA-LACTALBUMIN | Descriptor: | CALCIUM ION, PROTEIN (ALPHA-LACTALBUMIN) | Authors: | Horii, K, Matsushima, M, Tsumoto, K, Kumagai, I. | Deposit date: | 1998-11-26 | Release date: | 1999-11-26 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Effect of the extra n-terminal methionine residue on the stability and folding of recombinant alpha-lactalbumin expressed in Escherichia coli. J.Mol.Biol., 285, 1999
|
|
1IC4
| CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD32A)-HEN LYSOZYME COMPLEX | Descriptor: | IGG1 FAB CHAIN H, LYSOZYME BINDING IG KAPPA CHAIN, LYSOZYME C | Authors: | Shiroishi, M, Yokota, A, Tsumoto, K, Kondo, H, Nishimiya, Y, Horii, K, Matsushima, M, Ogasahara, K, Yutani, K, Kumagai, I. | Deposit date: | 2001-03-30 | Release date: | 2001-07-18 | Last modified: | 2021-11-10 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Structural evidence for entropic contribution of salt bridge formation to a protein antigen-antibody interaction: the case of hen lysozyme-HyHEL-10 Fv complex. J.Biol.Chem., 276, 2001
|
|
1IC7
| CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD32A99A)-HEN LYSOZYME COMPLEX | Descriptor: | IGG1 FAB CHAIN H, LYSOZYME BINDING IG KAPPA CHAIN, LYSOZYME C | Authors: | Shiroishi, M, Yokota, A, Tsumoto, K, Kondo, H, Nishimiya, Y, Horii, K, Matsushima, M, Ogasahara, K, Yutani, K, Kumagai, I. | Deposit date: | 2001-03-30 | Release date: | 2001-07-18 | Last modified: | 2021-11-10 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Structural evidence for entropic contribution of salt bridge formation to a protein antigen-antibody interaction: the case of hen lysozyme-HyHEL-10 Fv complex. J.Biol.Chem., 276, 2001
|
|
1IC5
| CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD99A)-HEN LYSOZYME COMPLEX | Descriptor: | IGG1 FAB CHAIN H, LYSOZYME BINDING IG KAPPA CHAIN, LYSOZYME C | Authors: | Shiroishi, M, Yokota, A, Tsumoto, K, Kondo, H, Nishimiya, Y, Horii, K, Matsushima, M, Ogasahara, K, Yutani, K, Kumagai, I. | Deposit date: | 2001-03-30 | Release date: | 2001-07-18 | Last modified: | 2021-11-10 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structural evidence for entropic contribution of salt bridge formation to a protein antigen-antibody interaction: the case of hen lysozyme-HyHEL-10 Fv complex. J.Biol.Chem., 276, 2001
|
|
8J81
| MDM2 bound with a peptoid | Descriptor: | (2S)-2-[[(2S)-2-[(6-chloranyl-1H-indol-3-yl)methyl-[(2S)-2-[[(2S)-2-[ethanoyl-(phenylmethyl)amino]propanoyl]-methyl-amino]propanoyl]amino]propanoyl]-methyl-amino]-N-(3,3-dimethylbutyl)-N-[(2S)-1-oxidanylidene-1-piperazin-1-yl-propan-2-yl]propanamide, CHLORIDE ION, E3 ubiquitin-protein ligase Mdm2 | Authors: | Yokomine, M, Fukuda, Y, Ago, H, Matsuura, H, Ueno, G, Nagatoishi, S, Yamamoto, M, Tsumoto, K, Jumpei, M, Sando, S. | Deposit date: | 2023-04-28 | Release date: | 2024-05-01 | Method: | X-RAY DIFFRACTION (1.35 Å) | Cite: | A structural and physicochemical study of how a peptoid binds to a protein To Be Published
|
|
8H62
| Crystal structure of Internalin A from Listeria monocytogenes with human E-cadherin EC12 | Descriptor: | ACETATE ION, CALCIUM ION, Cadherin-1, ... | Authors: | Caaveiro, J.M.M, Nagatoish, S, Tsumoto, K. | Deposit date: | 2022-10-14 | Release date: | 2023-10-04 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.91 Å) | Cite: | Anti-InlA single-domain antibodies that inhibit the cell invasion of Listeria monocytogenes. J.Biol.Chem., 299, 2023
|
|