1BDD
 
 | | STAPHYLOCOCCUS AUREUS PROTEIN A, IMMUNOGLOBULIN-BINDING B DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE | | Descriptor: | STAPHYLOCOCCUS AUREUS PROTEIN A | | Authors: | Gouda, H, Torigoe, H, Saito, A, Sato, M, Arata, Y, Shimada, I. | | Deposit date: | 1996-06-28 | | Release date: | 1997-01-11 | | Last modified: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures.
Biochemistry, 31, 1992
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1BDC
 | | STAPHYLOCOCCUS AUREUS PROTEIN A, IMMUNOGLOBULIN-BINDING B DOMAIN, NMR, 10 STRUCTURES | | Descriptor: | STAPHYLOCOCCUS AUREUS PROTEIN A | | Authors: | Gouda, H, Torigoe, H, Saito, A, Sato, M, Arata, Y, Shimada, I. | | Deposit date: | 1996-06-28 | | Release date: | 1997-01-11 | | Last modified: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures.
Biochemistry, 31, 1992
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8DYJ
 | | Crystal structure of human methylmalonyl-CoA mutase in complex with ADP and cob(II)alamin | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, COBALAMIN, Methylmalonyl-CoA mutase, ... | | Authors: | Mascarenhas, R.N, Gouda, H, Banerjee, R. | | Deposit date: | 2022-08-04 | | Release date: | 2023-07-12 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Bivalent molecular mimicry by ADP protects metal redox state and promotes coenzyme B 12 repair.
Proc.Natl.Acad.Sci.USA, 120, 2023
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8DYL
 | | Crystal structure of human methylmalonyl-CoA mutase bound to aquocobalamin | | Descriptor: | COBALAMIN, GLYCEROL, Methylmalonyl-CoA mutase, ... | | Authors: | Mascarenhas, R.N, Gouda, H, Banerjee, R. | | Deposit date: | 2022-08-04 | | Release date: | 2023-07-12 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Bivalent molecular mimicry by ADP protects metal redox state and promotes coenzyme B 12 repair.
Proc.Natl.Acad.Sci.USA, 120, 2023
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7RUV
 | | Structure of Human ATP:Cobalamin Adenosyltransferase E193K bound to adenosylcobalamin | | Descriptor: | 5'-DEOXYADENOSINE, COBALAMIN, Corrinoid adenosyltransferase, ... | | Authors: | Mascarenhas, R, Gouda, H, Koutmos, M, Banerjee, R. | | Deposit date: | 2021-08-18 | | Release date: | 2021-11-24 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Patient mutations in human ATP:cob(I)alamin adenosyltransferase differentially affect its catalytic versus chaperone functions.
J.Biol.Chem., 297, 2021
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7RUU
 | | Structure of Human ATP:Cobalamin Adenosyltransferase R190C bound to adenosylcobalamin | | Descriptor: | 5'-DEOXYADENOSINE, ACETATE ION, COBALAMIN, ... | | Authors: | Mascarenhas, R, Gouda, H, Koutmos, M, Banerjee, R. | | Deposit date: | 2021-08-18 | | Release date: | 2021-11-24 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Patient mutations in human ATP:cob(I)alamin adenosyltransferase differentially affect its catalytic versus chaperone functions.
J.Biol.Chem., 297, 2021
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7RUT
 | | Structure of Human ATP:Cobalamin Adenosyltransferase R190C bound to ATP | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, Corrinoid adenosyltransferase, GLYCEROL, ... | | Authors: | Mascarenhas, R, Gouda, H, Koutmos, M, Banerjee, R. | | Deposit date: | 2021-08-18 | | Release date: | 2021-11-24 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Patient mutations in human ATP:cob(I)alamin adenosyltransferase differentially affect its catalytic versus chaperone functions.
J.Biol.Chem., 297, 2021
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8GJU
 | | Crystal structure of human methylmalonyl-CoA mutase (MMUT) in complex with methylmalonic acidemia type A protein (MMAA), coenzyme A, and GDP | | Descriptor: | COENZYME A, GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... | | Authors: | Mascarenhas, R.M, Ruetz, M, Gouda, H, Yaw, M, Banerjee, R. | | Deposit date: | 2023-03-16 | | Release date: | 2023-08-09 | | Last modified: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (2.79 Å) | | Cite: | Architecture of the human G-protein-methylmalonyl-CoA mutase nanoassembly for B 12 delivery and repair.
Nat Commun, 14, 2023
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1OAW
 | | OMEGA-AGATOXIN IVA | | Descriptor: | OMEGA-AGATOXIN IVA | | Authors: | Kim, J.I, Konishi, S, Iwai, H, Kohno, T, Gouda, H, Shimada, I, Sato, K, Arata, Y. | | Deposit date: | 1995-06-28 | | Release date: | 1995-10-15 | | Last modified: | 2024-10-09 | | Method: | SOLUTION NMR | | Cite: | Three-dimensional solution structure of the calcium channel antagonist omega-agatoxin IVA: consensus molecular folding of calcium channel blockers.
J.Mol.Biol., 250, 1995
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1OAV
 | | OMEGA-AGATOXIN IVA | | Descriptor: | OMEGA-AGATOXIN IVA | | Authors: | Kim, J.I, Konishi, S, Iwai, H, Kohno, T, Gouda, H, Shimada, I, Sato, K, Arata, Y. | | Deposit date: | 1995-06-28 | | Release date: | 1995-10-15 | | Last modified: | 2024-10-30 | | Method: | SOLUTION NMR | | Cite: | Three-dimensional solution structure of the calcium channel antagonist omega-agatoxin IVA: consensus molecular folding of calcium channel blockers.
J.Mol.Biol., 250, 1995
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3WD4
 | | Serratia marcescens Chitinase B complexed with azide inhibitor and quinoline compound | | Descriptor: | (E)-N-(prop-2-en-1-yloxy)-1-(quinolin-4-yl)methanimine, Chitinase B, GLYCEROL, ... | | Authors: | Hirose, T, Maita, N, Gouda, H, Koseki, J, Yamamoto, T, Sugawara, A, Nakano, H, Hirono, S, Shiomi, K, Watanabe, T, Taniguchi, H, Sharpless, K.B, Omura, S, Sunazuka, T. | | Deposit date: | 2013-06-06 | | Release date: | 2013-09-18 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Observation of the controlled assembly of preclick components in the in situ click chemistry generation of a chitinase inhibitor
Proc.Natl.Acad.Sci.USA, 110, 2013
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3WD2
 | | Serratia marcescens Chitinase B complexed with azide inhibitor | | Descriptor: | Chitinase B, DITHIANE DIOL, GLYCEROL, ... | | Authors: | Hirose, T, Maita, N, Gouda, H, Koseki, J, Yamamoto, T, Sugawara, A, Nakano, H, Hirono, S, Shiomi, K, Watanabe, T, Taniguchi, H, Sharpless, K.B, Omura, S, Sunazuka, T. | | Deposit date: | 2013-06-06 | | Release date: | 2013-09-18 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Observation of the controlled assembly of preclick components in the in situ click chemistry generation of a chitinase inhibitor
Proc.Natl.Acad.Sci.USA, 110, 2013
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3WD1
 | | Serratia marcescens Chitinase B complexed with syn-triazole inhibitor | | Descriptor: | Chitinase B, GLYCEROL, N,N-dibenzyl-N~5~-[N-(methylcarbamoyl)carbamimidoyl]-N~2~-{[5-({[(E)-(quinolin-4-ylmethylidene)amino]oxy}methyl)-1H-1,2,3-triazol-1-yl]acetyl}-L-ornithinamide, ... | | Authors: | Hirose, T, Maita, N, Gouda, H, Koseki, J, Yamamoto, T, Sugawara, A, Nakano, H, Hirono, S, Shiomi, K, Watanabe, T, Taniguchi, H, Sharpless, K.B, Omura, S, Sunazuka, T. | | Deposit date: | 2013-06-06 | | Release date: | 2013-09-18 | | Last modified: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Observation of the controlled assembly of preclick components in the in situ click chemistry generation of a chitinase inhibitor
Proc.Natl.Acad.Sci.USA, 110, 2013
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3WD3
 | | Serratia marcescens Chitinase B complexed with azide inhibitor | | Descriptor: | Chitinase B, GLYCEROL, SULFATE ION, ... | | Authors: | Hirose, T, Maita, N, Gouda, H, Koseki, J, Yamamoto, T, Sugawara, A, Nakano, H, Hirono, S, Shiomi, K, Watanabe, T, Taniguchi, H, Sharpless, K.B, Omura, S, Sunazuka, T. | | Deposit date: | 2013-06-06 | | Release date: | 2013-09-18 | | Last modified: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Observation of the controlled assembly of preclick components in the in situ click chemistry generation of a chitinase inhibitor
Proc.Natl.Acad.Sci.USA, 110, 2013
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3WD0
 | | Serratia marcescens Chitinase B, tetragonal form | | Descriptor: | Chitinase B, DITHIANE DIOL, GLYCEROL, ... | | Authors: | Hirose, T, Maita, N, Gouda, H, Koseki, J, Yamamoto, T, Sugawara, A, Nakano, H, Hirono, S, Shiomi, K, Watanabe, T, Taniguchi, H, Sharpless, K.B, Omura, S, Sunazuka, T. | | Deposit date: | 2013-06-06 | | Release date: | 2013-09-18 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Observation of the controlled assembly of preclick components in the in situ click chemistry generation of a chitinase inhibitor
Proc.Natl.Acad.Sci.USA, 110, 2013
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7DKD
 | | Stenotrophomonas maltophilia DPP7 in complex with Asn-Tyr | | Descriptor: | ASPARAGINE, Dipeptidyl-peptidase, GLYCEROL, ... | | Authors: | Sakamoto, Y, Nakamura, A, Suzuki, Y, Honma, N, Roppongi, S, Kushibiki, C, Yonezawa, N, Takahashi, M, Shida, Y, Gouda, H, Nonaka, T, Ogasawara, W, Tanaka, N. | | Deposit date: | 2020-11-23 | | Release date: | 2021-11-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.92 Å) | | Cite: | Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7.
Sci Rep, 11, 2021
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7DKC
 | | Stenotrophomonas maltophilia DPP7 in complex with Tyr-Tyr | | Descriptor: | Dipeptidyl-peptidase, GLYCEROL, TYROSINE | | Authors: | Sakamoto, Y, Nakamura, A, Suzuki, Y, Honma, N, Roppongi, S, Kushibiki, C, Yonezawa, N, Takahashi, M, Shida, Y, Gouda, H, Nonaka, T, Ogasawara, W, Tanaka, N. | | Deposit date: | 2020-11-23 | | Release date: | 2021-11-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.86 Å) | | Cite: | Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7.
Sci Rep, 11, 2021
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7DKE
 | | Stenotrophomonas maltophilia DPP7 in complex with Phe-Tyr | | Descriptor: | Dipeptidyl-peptidase, GLYCEROL, PHENYLALANINE, ... | | Authors: | Sakamoto, Y, Nakamura, A, Suzuki, Y, Honma, N, Roppongi, S, Kushibiki, C, Yonezawa, N, Takahashi, M, Shida, Y, Gouda, H, Nonaka, T, Ogasawara, W, Tanaka, N. | | Deposit date: | 2020-11-23 | | Release date: | 2021-11-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (1.91 Å) | | Cite: | Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7.
Sci Rep, 11, 2021
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7DKB
 | | Stenotrophomonas maltophilia DPP7 in complex with Val-Tyr | | Descriptor: | Dipeptidyl-peptidase, TYROSINE, VALINE | | Authors: | Sakamoto, Y, Nakamura, A, Suzuki, Y, Honma, N, Roppongi, S, Kushibiki, C, Yonezawa, N, Takahashi, M, Shida, Y, Gouda, H, Nonaka, T, Ogasawara, W, Tanaka, N. | | Deposit date: | 2020-11-23 | | Release date: | 2021-11-03 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.03 Å) | | Cite: | Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7.
Sci Rep, 11, 2021
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5X2L
 | | Crystal Structure of Human Serine Racemase | | Descriptor: | MAGNESIUM ION, PYRIDOXAL-5'-PHOSPHATE, Serine racemase | | Authors: | Obita, T, Matsumoto, K, Mori, H, Toyooka, N, Mizuguchi, M. | | Deposit date: | 2017-02-01 | | Release date: | 2018-01-31 | | Last modified: | 2021-02-24 | | Method: | X-RAY DIFFRACTION (1.806 Å) | | Cite: | Design, synthesis, and evaluation of novel inhibitors for wild-type human serine racemase.
Bioorg. Med. Chem. Lett., 2017
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6OXC
 | | Structure of Mycobacterium tuberculosis methylmalonyl-CoA mutase with adenosyl cobalamin | | Descriptor: | 5'-DEOXYADENOSINE, COBALAMIN, Methylmalonyl-CoA mutase large subunit, ... | | Authors: | Purchal, M, Ruetz, M, Banerjee, R, Koutmos, M. | | Deposit date: | 2019-05-13 | | Release date: | 2019-11-13 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Itaconyl-CoA forms a stable biradical in methylmalonyl-CoA mutase and derails its activity and repair.
Science, 366, 2019
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6OXD
 | | Structure of Mycobacterium tuberculosis methylmalonyl-CoA mutase with adenosyl cobalamin | | Descriptor: | 5'-DEOXYADENOSINE, COBALAMIN, Itaconyl coenzyme A, ... | | Authors: | Purchal, M, Ruetz, M, Banerjee, R, Koutmos, M. | | Deposit date: | 2019-05-13 | | Release date: | 2019-11-13 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Itaconyl-CoA forms a stable biradical in methylmalonyl-CoA mutase and derails its activity and repair.
Science, 366, 2019
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4Y04
 | | Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis (Space) | | Descriptor: | GLYCEROL, POTASSIUM ION, Peptidase S46 | | Authors: | Sakamoto, Y, Suzuki, Y, Iizuka, I, Tateoka, C, Roppongi, S, Fujimoto, M, Inaka, K, Tanaka, H, Yamada, M, Ohta, K, Nonaka, T, Ogasawara, W, Tanaka, N. | | Deposit date: | 2015-02-05 | | Release date: | 2015-07-15 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.66 Å) | | Cite: | Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity.
Sci Rep, 5, 2015
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6JTB
 | | Crystal structure of dipeptidyl peptidase 11 (DPP11) with citrate from Porphyromonas gingivalis (Space) | | Descriptor: | Asp/Glu-specific dipeptidyl-peptidase, CITRIC ACID, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Sakamoto, Y, Suzuki, Y, Iizuka, I, Roppongi, S, Kushibiki, C, Nakamura, A, Ogasawara, W, Tanaka, N. | | Deposit date: | 2019-04-10 | | Release date: | 2019-10-02 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Fragment-based discovery of the first nonpeptidyl inhibitor of an S46 family peptidase.
Sci Rep, 9, 2019
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6JTC
 | | Crystal structure of dipeptidyl peptidase 11 (DPP11) with SH-5 from Porphyromonas gingivalis (Space) | | Descriptor: | 2-(2-azanylethylamino)-5-nitro-benzoic acid, Asp/Glu-specific dipeptidyl-peptidase, GLYCEROL | | Authors: | Sakamoto, Y, Suzuki, Y, Iizuka, I, Roppongi, S, Kushibiki, C, Nakamura, A, Ogasawara, W, Tanaka, N. | | Deposit date: | 2019-04-10 | | Release date: | 2019-10-02 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (2.39 Å) | | Cite: | Fragment-based discovery of the first nonpeptidyl inhibitor of an S46 family peptidase.
Sci Rep, 9, 2019
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