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PDB: 53012 results

7QOH
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BU of 7qoh by Molmil
Unique vertex of the phicrAss001 virion with C5 symmetry imposed
Descriptor: Auxiliary capsid protein gp36, Head fiber trimer protein gp21, MAGNESIUM ION, ...
Authors:Bayfield, O.W, Shkoporov, A.N, Yutin, N, Khokhlova, E.V, Smith, J.L.R, Hawkins, D.E.D.P, Koonin, E.V, Hill, C, Antson, A.A.
Deposit date:2021-12-24
Release date:2023-03-29
Last modified:2023-05-24
Method:ELECTRON MICROSCOPY (3.32 Å)
Cite:Structural atlas of a human gut crassvirus.
Nature, 617, 2023
6W1O
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RT XFEL structure of the dark-stable state of Photosystem II (0F, S1-rich) at 2.08 Angstrom resolution
Descriptor: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ...
Authors:Ibrahim, M, Fransson, T, Chatterjee, R, Cheah, M.H, Hussein, R, Lassalle, L, Sutherlin, K.D, Young, I.D, Fuller, F.D, Gul, S, Kim, I.-S, Simon, P.S, de Lichtenberg, C, Chernev, P, Bogacz, I, Pham, C, Orville, A.M, Saichek, N, Northen, T.R, Batyuk, A, Carbajo, S, Alonso-Mori, R, Tono, K, Owada, S, Bhowmick, A, Bolotovski, R, Mendez, D, Moriarty, N.W, Holton, J.M, Dobbek, H, Brewster, A.S, Adams, P.D, Sauter, N.K, Bergmann, U, Zouni, A, Messinger, J, Kern, J, Yachandra, V.K, Yano, J.
Deposit date:2020-03-04
Release date:2020-05-20
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.08 Å)
Cite:Untangling the sequence of events during the S2→ S3transition in photosystem II and implications for the water oxidation mechanism.
Proc.Natl.Acad.Sci.USA, 117, 2020
7QOK
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BU of 7qok by Molmil
Tail muzzle assembly of the phicrAss001 virion with C6 symmetry imposed
Descriptor: MAGNESIUM ION, Muzzle bound helix, Muzzle protein gp44, ...
Authors:Bayfield, O.W, Shkoporov, A.N, Yutin, N, Khokhlova, E.V, Smith, J.L.R, Hawkins, D.E.D.P, Koonin, E.V, Hill, C, Antson, A.A.
Deposit date:2021-12-24
Release date:2023-03-29
Last modified:2024-07-17
Method:ELECTRON MICROSCOPY (3.38 Å)
Cite:Structural atlas of a human gut crassvirus.
Nature, 617, 2023
7QOL
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BU of 7qol by Molmil
Tail assembly of the phicrAss001 virion with C6 symmetry imposed
Descriptor: Cargo protein 1 gp45, MAGNESIUM ION, Muzzle bound helix, ...
Authors:Bayfield, O.W, Shkoporov, A.N, Yutin, N, Khokhlova, E.V, Smith, J.L.R, Hawkins, D.E.D.P, Koonin, E.V, Hill, C, Antson, A.A.
Deposit date:2021-12-24
Release date:2023-03-29
Last modified:2023-05-24
Method:ELECTRON MICROSCOPY (3.33 Å)
Cite:Structural atlas of a human gut crassvirus.
Nature, 617, 2023
6NM4
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BU of 6nm4 by Molmil
Crystal structure of SAM-bound PRDM9 in complex with MRK-740 inhibitor
Descriptor: 4-[3-(3,5-dimethoxyphenyl)-1,2,4-oxadiazol-5-yl]-1-methyl-9-(2-methylpyridin-4-yl)-1,4,9-triazaspiro[5.5]undecane, Histone-lysine N-methyltransferase PRDM9, S-ADENOSYLMETHIONINE, ...
Authors:Ivanochko, D, Halabelian, L, Fischer, C, Sanders, J.M, Kattar, S.D, Brown, P.J, Edwards, A.M, Bountra, C, Arrowsmith, C.H, Structural Genomics Consortium (SGC)
Deposit date:2019-01-10
Release date:2019-02-13
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.58 Å)
Cite:Discovery of a chemical probe for PRDM9.
Nat Commun, 10, 2019
7AEG
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BU of 7aeg by Molmil
SARS-CoV-2 main protease in a covalent complex with SDZ 224015 derivative, compound 5
Descriptor: 3C-like proteinase, DIMETHYL SULFOXIDE, N-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamide
Authors:Owen, C.D, Redhead, M.A, Lukacik, P, Strain-Damerell, C, Fearon, D, Brewitz, L, Collette, A, Robinson, C, Collins, P, Radoux, C, Navratilova, I, Douangamath, A, von Delft, F, Malla, T.R, Nugen, T, Hull, H, Tumber, A, Schofield, C.J, Hallet, D, Stuart, D.I, Hopkins, A.L, Walsh, M.A.
Deposit date:2020-09-17
Release date:2021-07-07
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Bispecific repurposed medicines targeting the viral and immunological arms of COVID-19.
Sci Rep, 11, 2021
8DAQ
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BU of 8daq by Molmil
CryoEM structure of Western equine encephalitis virus VLP
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, E1 envelope glycoprotein, E2 envelope glycoprotein
Authors:Zimmerman, M.I, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Biology of Infectious Diseases (CSBID)
Deposit date:2022-06-13
Release date:2023-12-20
Method:ELECTRON MICROSCOPY (4.35 Å)
Cite:Alternate repeat domain usage in an alphavirus entry receptor enables host species expansion
To Be Published
8DAN
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BU of 8dan by Molmil
CryoEM structure of Western equine encephalitis virus VLP in complex with the avian MXRA8 receptor
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, E1 envelope glycoprotein, E2 envelope glycoprotein, ...
Authors:Zimmerman, M.I, Fremont, D.H, Center for Structural Genomics of Infectious Diseases (CSGID), Center for Structural Biology of Infectious Diseases (CSBID)
Deposit date:2022-06-13
Release date:2023-12-20
Method:ELECTRON MICROSCOPY (4.74 Å)
Cite:Alternate domain repeat usage in an alphavirus entry receptor enables host species expansion
To Be Published
8FY0
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BU of 8fy0 by Molmil
E3:PROTAC:target ternary complex structure (VCB/753b/BCL-xL)
Descriptor: Bcl-2-like protein 1, CACODYLIC ACID, Elongin-B, ...
Authors:Olsen, S.K, Nayak, D, Lv, D, Yuan, Y, Zhang, P, Hu, W, Lv, Z, Sung, P, Hromas, R, Zheng, G, Zhou, D.
Deposit date:2023-01-25
Release date:2024-04-10
Method:X-RAY DIFFRACTION (2.94 Å)
Cite:Development and crystal structures of a potent second-generation dual degrader of BCL-2 and BCL-xL.
Nat Commun, 15, 2024
7AEH
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BU of 7aeh by Molmil
SARS-CoV-2 main protease in a covalent complex with a pyridine derivative of ABT-957, compound 1
Descriptor: (2~{R})-5-oxidanylidene-~{N}-[(2~{R},3~{S})-3-oxidanyl-4-oxidanylidene-1-phenyl-4-(pyridin-2-ylmethylamino)butan-2-yl]-1-(phenylmethyl)pyrrolidine-2-carboxamide, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE
Authors:Owen, C.D, Redhead, M.A, Lukacik, P, Strain-Damerell, C, Fearon, D, Brewitz, L, Collette, A, Robinson, C, Collins, P, Radoux, C, Navratilova, I, Douangamath, A, von Delft, F, Malla, T.R, Nugen, T, Hull, H, Tumber, A, Schofield, C.J, Hallet, D, Stuart, D.I, Hopkins, A.L, Walsh, M.A.
Deposit date:2020-09-17
Release date:2021-07-07
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (1.3 Å)
Cite:Bispecific repurposed medicines targeting the viral and immunological arms of COVID-19.
Sci Rep, 11, 2021
6YH0
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BU of 6yh0 by Molmil
Marasmius oreades agglutinin (MOA) in complex with the truncated PVPRAHS synthetic substrate
Descriptor: Agglutinin, CALCIUM ION, CHLORIDE ION, ...
Authors:Cordara, G, Manna, D, Krengel, U.
Deposit date:2020-03-28
Release date:2020-07-29
Last modified:2024-01-24
Method:X-RAY DIFFRACTION (1.56 Å)
Cite:Crystal structure of MOA in complex with a peptide fragment: A protease caught in flagranti .
Curr Res Struct Biol, 2, 2020
7ONS
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BU of 7ons by Molmil
PARP1 catalytic domain in complex with isoquinolone-based inhibitor (compound 16)
Descriptor: 7-[[4-(1,5-dimethylimidazol-2-yl)piperazin-1-yl]methyl]-3-ethyl-1~{H}-quinolin-2-one, Poly [ADP-ribose] polymerase 1, SULFATE ION
Authors:Schimpl, M, Balazs, A, Barratt, D, Bista, M, Chuba, M, Degorce, S.L, Di Fruscia, P, Embrey, K, Ghosh, A, Gill, S, Gunnarsson, A, Hande, S, Hemsley, P, Heightman, T.D, Illuzzi, G, Lane, J, Larner, C, Leo, E, Madin, A, Martin, S, McWilliams, L, Orme, J, Pachl, F, Packer, M, Pike, A, Staniszewska, A.D, Talbot, V, Underwood, E, Varnes, G.J, Zhang, A, Zheng, X, Johannes, J.W.
Deposit date:2021-05-25
Release date:2021-09-15
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (1.97 Å)
Cite:Discovery of 5-{4-[(7-Ethyl-6-oxo-5,6-dihydro-1,5-naphthyridin-3-yl)methyl]piperazin-1-yl}- N -methylpyridine-2-carboxamide (AZD5305): A PARP1-DNA Trapper with High Selectivity for PARP1 over PARP2 and Other PARPs.
J.Med.Chem., 64, 2021
7OX8
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BU of 7ox8 by Molmil
Target-bound SpCas9 complex with TRAC full RNA guide
Descriptor: CRISPR-associated endonuclease Cas9/Csn1, MAGNESIUM ION, POTASSIUM ION, ...
Authors:Donohoue, P, Pacesa, M, Lau, E, Vidal, B, Irby, M.J, Nyer, D.B, Rotstein, T, Banh, L, Toh, M.T, Gibson, J, Kohrs, B, Baek, K, Owen, A.L.G, Slorach, E.M, van Overbeek, M, Fuller, C.K, May, A.P, Jinek, M, Cameron, P.
Deposit date:2021-06-22
Release date:2021-09-15
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (2.75 Å)
Cite:Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells.
Mol.Cell, 81, 2021
7ONT
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BU of 7ont by Molmil
PARP1 catalytic domain in complex with a selective pyridine carboxamide-based inhibitor (compound 22)
Descriptor: 5-[4-[(3-ethyl-2-oxidanylidene-1~{H}-quinolin-7-yl)methyl]piperazin-1-yl]-~{N}-methyl-pyridine-2-carboxamide, Poly [ADP-ribose] polymerase 1, SULFATE ION
Authors:Schimpl, M, Balazs, A, Barratt, D, Bista, M, Chuba, M, Degorce, S.L, Di Fruscia, P, Embrey, K, Ghosh, A, Gill, S, Gunnarsson, A, Hande, S, Hemsley, P, Heightman, T.D, Illuzzi, G, Lane, J, Larner, C, Leo, E, Madin, A, Martin, S, McWilliams, L, Orme, J, Pachl, F, Packer, M.J, Pike, A, Staniszewska, A.D, Talbot, V, Underwood, E, Varnes, G.J, Zhang, A, Zheng, X, Johannes, J.W.
Deposit date:2021-05-25
Release date:2021-09-15
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (1.853 Å)
Cite:Discovery of 5-{4-[(7-Ethyl-6-oxo-5,6-dihydro-1,5-naphthyridin-3-yl)methyl]piperazin-1-yl}- N -methylpyridine-2-carboxamide (AZD5305): A PARP1-DNA Trapper with High Selectivity for PARP1 over PARP2 and Other PARPs.
J.Med.Chem., 64, 2021
8G5B
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BU of 8g5b by Molmil
Influenza A H3N2 X-31 Hemagglutinin in complex with FL-1061
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, FL-1061 heavy chain, FL-1061 light chain, ...
Authors:Windsor, I.W, Thornlow, D, Schmidt, A.G.
Deposit date:2023-02-12
Release date:2024-02-21
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:Fabs elicited by hyperglycosylated immunogen
To Be Published
7OX7
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BU of 7ox7 by Molmil
Target-bound SpCas9 complex with TRAC chimeric RNA-DNA guide
Descriptor: CRISPR-associated endonuclease Cas9/Csn1, MAGNESIUM ION, POTASSIUM ION, ...
Authors:Donohoue, P, Pacesa, M, Lau, E, Vidal, B, Irby, M.J, Nyer, D.B, Rotstein, T, Banh, L, Toh, M.T, Gibson, J, Kohrs, B, Baek, K, Owen, A.L.G, Slorach, E.M, van Overbeek, M, Fuller, C.K, May, A.P, Jinek, M, Cameron, P.
Deposit date:2021-06-22
Release date:2021-09-15
Last modified:2024-01-31
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Conformational control of Cas9 by CRISPR hybrid RNA-DNA guides mitigates off-target activity in T cells.
Mol.Cell, 81, 2021
8G5A
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BU of 8g5a by Molmil
X-31 hemagglutinin in complex with FL-1061 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, FL-1086 Fab heavy chain, FL-1086 light chain, ...
Authors:Windsor, I.W, Thornlow, D, Schmidt, A.G.
Deposit date:2023-02-12
Release date:2024-02-21
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Antibodies elicited by a hyperglycoslated immunogen
To Be Published
7ONR
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BU of 7onr by Molmil
PARP1 catalytic domain in complex with 8-chloroquinazolinone-based inhibitor (compound 9)
Descriptor: 8-chloranyl-2-[3-[4-(1,5-dimethylimidazol-2-yl)piperazin-1-yl]propyl]-3~{H}-quinazolin-4-one, Poly [ADP-ribose] polymerase 1, SULFATE ION
Authors:Schimpl, M, Balazs, A, Barratt, D, Bista, M, Chuba, M, Degorce, S.L, Di Fruscia, P, Embrey, K, Ghosh, A, Gill, S, Gunnarsson, A, Hande, S, Hemsley, P, Illuzzi, G, Lane, J, Larner, C, Leo, E, Madin, A, Martin, S, McWilliams, L, Orme, J, Pachl, F, Packer, M, Pike, A, Staniszewska, A.D, Talbot, V, Underwood, E, Varnes, G.J, Zhang, A, Zheng, X, Johannes, J.W.
Deposit date:2021-05-25
Release date:2021-09-15
Last modified:2024-05-01
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:Discovery of 5-{4-[(7-Ethyl-6-oxo-5,6-dihydro-1,5-naphthyridin-3-yl)methyl]piperazin-1-yl}- N -methylpyridine-2-carboxamide (AZD5305): A PARP1-DNA Trapper with High Selectivity for PARP1 over PARP2 and Other PARPs.
J.Med.Chem., 64, 2021
8GF5
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BU of 8gf5 by Molmil
McrD binds asymmetrically to methyl-coenzyme M reductase improving active site accessibility during assembly
Descriptor: 1-THIOETHANESULFONIC ACID, Coenzyme B, FACTOR 430, ...
Authors:Joiner, A.M.N, Chadwick, G.L, Nayak, D.D.
Deposit date:2023-03-07
Release date:2023-06-28
Method:ELECTRON MICROSCOPY (3 Å)
Cite:McrD binds asymmetrically to methyl-coenzyme M reductase improving active-site accessibility during assembly.
Proc.Natl.Acad.Sci.USA, 120, 2023
8GF6
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BU of 8gf6 by Molmil
Apo-apo MCR assembly intermediate
Descriptor: Methyl coenzyme M reductase, subunit D, Methyl-coenzyme M reductase subunit alpha, ...
Authors:Joiner, A.M.N, Chadwick, G.L, Nayak, D.D.
Deposit date:2023-03-07
Release date:2023-06-28
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:McrD binds asymmetrically to methyl-coenzyme M reductase improving active-site accessibility during assembly.
Proc.Natl.Acad.Sci.USA, 120, 2023
8GEP
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BU of 8gep by Molmil
SULFITE REDUCTASE HEMOPROTEIN NITRATE COMPLEX
Descriptor: IRON/SULFUR CLUSTER, NITRATE ION, POTASSIUM ION, ...
Authors:Crane, B.R, Getzoff, E.D.
Deposit date:1997-07-11
Release date:1998-01-14
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Probing the catalytic mechanism of sulfite reductase by X-ray crystallography: structures of the Escherichia coli hemoprotein in complex with substrates, inhibitors, intermediates, and products.
Biochemistry, 36, 1997
6O38
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BU of 6o38 by Molmil
Structure of a chaperone-substrate complex
Descriptor: Acinetobacter secreted protease CpaA, SULFATE ION, Type II secretion chaperone CpaB, ...
Authors:Urusova, D.V, Tolia, N.H.
Deposit date:2019-02-26
Release date:2019-07-24
Last modified:2019-09-25
Method:X-RAY DIFFRACTION (2.595 Å)
Cite:The structure ofAcinetobacter-secreted protease CpaA complexed with its chaperone CpaB reveals a novel mode of a T2SS chaperone-substrate interaction.
J.Biol.Chem., 294, 2019
6O3C
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BU of 6o3c by Molmil
Crystal structure of active Smoothened bound to SAG21k, cholesterol, and NbSmo8
Descriptor: (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose, 3-chloro-4,7-difluoro-N-{[2-methoxy-5-(pyridin-4-yl)phenyl]methyl}-N-[trans-4-(methylamino)cyclohexyl]-1-benzothiophene-2-carboxamide, ...
Authors:Deshpande, I.S, Liang, J, Hedeen, D, Roberts, K.J, Zhang, Y, Ha, B, Latorraca, N.R, Faust, B, Dror, R.O, Beachy, P.A, Myers, B.R, Manglik, A.
Deposit date:2019-02-26
Release date:2019-07-03
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Smoothened stimulation by membrane sterols drives Hedgehog pathway activity.
Nature, 571, 2019
6W1V
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BU of 6w1v by Molmil
RT XFEL structure of the two-flash state of Photosystem II (2F, S3-rich) at 2.09 Angstrom resolution
Descriptor: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ...
Authors:Ibrahim, M, Fransson, T, Chatterjee, R, Cheah, M.H, Hussein, R, Lassalle, L, Sutherlin, K.D, Young, I.D, Fuller, F.D, Gul, S, Kim, I.-S, Simon, P.S, de Lichtenberg, C, Chernev, P, Bogacz, I, Pham, C, Orville, A.M, Saichek, N, Northen, T.R, Batyuk, A, Carbajo, S, Alonso-Mori, R, Tono, K, Owada, S, Bhowmick, A, Bolotovski, R, Mendez, D, Moriarty, N.W, Holton, J.M, Dobbek, H, Brewster, A.S, Adams, P.D, Sauter, N.K, Bergmann, U, Zouni, A, Messinger, J, Kern, J, Yachandra, V.K, Yano, J.
Deposit date:2020-03-04
Release date:2020-06-03
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.09 Å)
Cite:Untangling the sequence of events during the S2→ S3transition in photosystem II and implications for the water oxidation mechanism.
Proc.Natl.Acad.Sci.USA, 117, 2020
8R54
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BU of 8r54 by Molmil
Mouse teneurin-3 non-compact subunit - A0B0 isoform
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Teneurin-3, ...
Authors:Gogou, C, Meijer, D.H.
Deposit date:2023-11-15
Release date:2024-05-08
Method:ELECTRON MICROSCOPY (3.5 Å)
Cite:Alternative splicing controls teneurin-3 compact dimer formation for neuronal recognition.
Nat Commun, 15, 2024

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