Legacy flatfile-incompatible PDB entries

9B5J	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 5 map and model (Ub(A)-AMP) Descriptor: 4-aminobutanenitrile, ADENOSINE MONOPHOSPHATE, Large ribosomal subunit protein eL40B, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-18 Method: ELECTRON MICROSCOPY (2.86 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
9B5K	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 1 map and model from cluster 1 (Ub(A)/ATP/Mg) Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, Large ribosomal subunit protein eL40B, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-18 Method: ELECTRON MICROSCOPY (3.16 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
9B5L	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 10 map and model from cluster 5 (Ub(A)-AMP) Descriptor: 4-aminobutanenitrile, ADENOSINE MONOPHOSPHATE, Polyubiquitin, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-18 Method: ELECTRON MICROSCOPY (3.3 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
9B5M	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - consensus map and model Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-25 Method: ELECTRON MICROSCOPY (2.79 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
9B5N	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 1 map and model from consensus Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-25 Method: ELECTRON MICROSCOPY (3.12 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
9B5O	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 10 map and model from consensus Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-25 Method: ELECTRON MICROSCOPY (3.19 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
9B5P	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 1 map and model (ATP/Mg) Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-25 Method: ELECTRON MICROSCOPY (3.08 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
9B5Q	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 2 map and model (ATP/Mg) Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-25 Method: ELECTRON MICROSCOPY (2.95 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
9B5R	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 3 map and model (ATP/Mg) Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-25 Method: ELECTRON MICROSCOPY (2.95 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
9B5S	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 4 map and model (ATP/Mg) Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-25 Method: ELECTRON MICROSCOPY (2.96 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
9B5T	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 5 map and model (ATP/Mg) Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-25 Method: ELECTRON MICROSCOPY (3.16 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
9B5U	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 1 map and model from cluster 1 (ATP/Mg) Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-25 Method: ELECTRON MICROSCOPY (3.67 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
9B5V	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 10 map and model from cluster 1 (ATP/Mg) Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-25 Method: ELECTRON MICROSCOPY (3.94 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
9B5W	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 1 map and model from cluster 5 (ATP/Mg) Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-25 Method: ELECTRON MICROSCOPY (3.96 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
9B5X	Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - Ub(T) class 10 map and model from cluster 5 (ATP/Mg) Descriptor: 4-aminobutanenitrile, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Kochanczyk, T, Lima, C.D. Deposit date: 2024-03-22 Release date: 2024-06-05 Last modified: 2024-09-25 Method: ELECTRON MICROSCOPY (4.16 Å) Cite: Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature, 633, 2024
9B6F	Cryo-EM structure of the mouse TRPM8 channel in complex with the antagonist AMG2850 Descriptor: (8R)-8-[4-(trifluoromethyl)phenyl]-N-[(2S)-1,1,1-trifluoropropan-2-yl]-5,8-dihydro-1,7-naphthyridine-7(6H)-carboxamide, CHOLESTEROL HEMISUCCINATE, Transient receptor potential cation channel subfamily M member 8 Authors: Yin, Y, Park, C.-G, Zhang, F, Fedor, J, Feng, S, Suo, Y, Im, W, Lee, S.-Y. Deposit date: 2024-03-25 Release date: 2024-08-21 Method: ELECTRON MICROSCOPY (3.42 Å) Cite: Mechanisms of sensory adaptation and inhibition of the cold and menthol receptor TRPM8. Sci Adv, 10, 2024
9B70	Cryo-EM structure of MraY in complex with analogue 2 Descriptor: (2~{S},3~{S})-3-[(2~{S},3~{R},4~{S},5~{R})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxy-2-[[3-[[[(2~{S})-6-azanyl-2-(hexadecanoylamino)hexanoyl]amino]methyl]phenyl]methylamino]-3-[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]propanoic acid, MraYAA nanobody, Phospho-N-acetylmuramoyl-pentapeptide-transferase Authors: Hao, A, Lee, S.-Y. Deposit date: 2024-03-26 Release date: 2024-06-26 Method: ELECTRON MICROSCOPY (2.88 Å) Cite: Development of a natural product optimization strategy for inhibitors against MraY, a promising antibacterial target. Nat Commun, 15, 2024
9B71	Cryo-EM structure of MraY in complex with analogue 3 Descriptor: (2~{S},3~{S})-3-[(2~{S},3~{R},4~{S},5~{R})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxy-3-[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]-2-[[4-[[[(2~{S})-5-carbamimidamido-2-(hexadecanoylamino)pentanoyl]amino]methyl]phenyl]methylamino]propanoic acid, MraYAA Nanobody, Phospho-N-acetylmuramoyl-pentapeptide-transferase Authors: Hao, A, Lee, S.-Y. Deposit date: 2024-03-26 Release date: 2024-06-26 Method: ELECTRON MICROSCOPY (2.7 Å) Cite: Development of a natural product optimization strategy for inhibitors against MraY, a promising antibacterial target. Nat Commun, 15, 2024
9B73	Cryo-EM structure of the desensitised ATP-bound human P2X1 receptor Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, ADENOSINE-5'-TRIPHOSPHATE, MAGNESIUM ION, ... Authors: Felix, M.B, Alisa, G, Hariprasad, V, Jesse, I.M, David, M.T. Deposit date: 2024-03-27 Release date: 2024-10-09 Method: ELECTRON MICROSCOPY (1.96 Å) Cite: Structural insights into the human P2X1 receptor and ligand interactions Nat Commun, 15, 2024
9B8P	Synaptic Vesicle V-ATPase with synaptophysin and SidK, State 3, V1 Descriptor: ADENOSINE-5'-DIPHOSPHATE, ATPase H+-transporting V1 subunit D, H(+)-transporting two-sector ATPase, ... Authors: Coupland, E.M, Rubinstein, J.L. Deposit date: 2024-03-31 Release date: 2024-07-03 Last modified: 2024-07-24 Method: ELECTRON MICROSCOPY (3.2 Å) Cite: High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles. Science, 385, 2024
9B95	Cryo-EM structure of the closed NF449-bound human P2X1 receptor Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 4,4',4'',4'''-{carbonylbis[azanediylbenzene-5,1,3-triylbis(carbonylazanediyl)]}tetra(benzene-1,3-disulfonic acid), P2X purinoceptor 1 Authors: Felix, M.B, Alisa, G, Hariprasad, V, Jesse, I.M, David, M.T. Deposit date: 2024-04-01 Release date: 2024-10-09 Method: ELECTRON MICROSCOPY (2.61 Å) Cite: Structural insights into the human P2X1 receptor and ligand interactions Nat Commun, 15, 2024
9B96	Crystal structure of the human PAD2 protein bound to inhibitor Descriptor: 1-({(2P)-1-{(1R)-1-(2-bromophenyl)-3-[5-(methanesulfonamido)-2-methylanilino]-3-oxopropyl}-2-[3-(4-chlorophenoxy)phenyl]-1H-1,3-benzimidazol-6-yl}methyl)-N-methyl-D-prolinamide, ACETATE ION, CALCIUM ION, ... Authors: Byrnes, L.J, Vajdos, F. Deposit date: 2024-04-01 Release date: 2024-10-09 Method: X-RAY DIFFRACTION (1.64 Å) Cite: Discovery, Characterization, and Structure of a Cell Active PAD2 Inhibitor Acting through a Novel Allosteric Mechanism. Acs Chem.Biol., 2024
9B97	Crystal structure of the human PAD2 protein bound to small molecule Descriptor: (1P)-N~3'~-[(2S)-3-cyclohexyl-1-(methylamino)-1-oxopropan-2-yl]-N~3~,N~3~-diethyl-4-fluoro-5'-{[4-(4-phenylbutyl)piperazin-1-yl]methyl}[1,1'-biphenyl]-3,3'-dicarboxamide, (4S)-2-METHYL-2,4-PENTANEDIOL, ACETATE ION, ... Authors: Byrnes, L.J, Vajdos, F. Deposit date: 2024-04-01 Release date: 2024-10-09 Method: X-RAY DIFFRACTION (1.95 Å) Cite: Discovery, Characterization, and Structure of a Cell Active PAD2 Inhibitor Acting through a Novel Allosteric Mechanism. Acs Chem.Biol., 2024
9B98	Crystal structure of the human PAD2 protein bound to small molecule Descriptor: (5P)-N,N-diethyl-2-fluoro-5-(2-[({1-[2-(methylamino)-2-oxoethyl]cyclohexyl}methyl)amino]-6-{methyl[1-(2-methyl-1-phenyl-1H-1,3-benzimidazole-5-carbonyl)piperidin-4-yl]amino}pyrimidin-4-yl)benzamide, ACETATE ION, CALCIUM ION, ... Authors: Byrnes, L.J, Vajdos, F. Deposit date: 2024-04-01 Release date: 2024-10-09 Method: X-RAY DIFFRACTION (2.003 Å) Cite: Discovery, Characterization, and Structure of a Cell Active PAD2 Inhibitor Acting through a Novel Allosteric Mechanism. Acs Chem.Biol., 2024
9B9N	Crystal structure of FlcD from Pseudomonas aeruginosa bound to iron (II) and substrate Descriptor: (2R)-2-{[(2Z)-2-(hydroxyimino)ethyl]sulfanyl}butanedioic acid, FE (III) ION, Pyrroloquinoline quinone (Coenzyme PQQ) biosynthesis protein C Authors: Walker, M.E, Grove, T.L, Li, B, Redinbo, M.R. Deposit date: 2024-04-02 Release date: 2024-07-31 Last modified: 2024-09-18 Method: X-RAY DIFFRACTION (2.28 Å) Cite: Structural Basis for Methine Excision by a Heme Oxygenase-like Enzyme. Acs Cent.Sci., 10, 2024

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