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Updated PDB entries
8SIR
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BU of 8sir by Molmil
Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with broadly neutralizing antibody CC25.54 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CC25.54 Fab heavy chain, CC25.54 Fab light chain, ...
Authors:Liu, H, Wilson, I.A.
Deposit date:2023-04-16
Release date:2024-03-13
Last modified:2025-07-30
Method:X-RAY DIFFRACTION (3.3 Å)
Cite:Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift.
Cell Rep, 44, 2025
8SIS
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BU of 8sis by Molmil
Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with broadly neutralizing antibody CC84.2 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CC84.2 Fab heavy chain, CC84.2 Fab light chain, ...
Authors:Liu, H, Wilson, I.A.
Deposit date:2023-04-16
Release date:2024-03-13
Last modified:2025-07-30
Method:X-RAY DIFFRACTION (3.08 Å)
Cite:Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift.
Cell Rep, 44, 2025
8SIT
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BU of 8sit by Molmil
Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with broadly neutralizing antibody CC84.24 Fab
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CC84.24 fab heavy chain, CC84.24 fab light chain, ...
Authors:Liu, H, Wilson, I.A.
Deposit date:2023-04-16
Release date:2024-03-13
Last modified:2025-07-30
Method:X-RAY DIFFRACTION (2.91 Å)
Cite:Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift.
Cell Rep, 44, 2025
8SKQ
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BU of 8skq by Molmil
RNA oligonucleotide containing an alpha-(L)-threofuranosyl nucleic acid (TNA)
Descriptor: TNA-containing RNA oligonucleotide
Authors:Harp, J.M, Egli, M.
Deposit date:2023-04-20
Release date:2024-02-14
Last modified:2025-07-30
Method:X-RAY DIFFRACTION (1.35 Å)
Cite:Shorter Is Better: The alpha-(l)-Threofuranosyl Nucleic Acid Modification Improves Stability, Potency, Safety, and Ago2 Binding and Mitigates Off-Target Effects of Small Interfering RNAs.
J.Am.Chem.Soc., 145, 2023
8T1U
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BU of 8t1u by Molmil
Crystal structure of the DRM2-CTA DNA complex
Descriptor: DNA (5'-D(P*AP*TP*TP*AP*TP*TP*AP*AP*TP*(C49)P*TP*AP*AP*AP*TP*TP*TP*A)-3'), DNA (5'-D(P*TP*AP*AP*AP*TP*TP*TP*AP*GP*AP*TP*TP*AP*AP*TP*AP*AP*T)-3'), DNA (cytosine-5)-methyltransferase DRM2, ...
Authors:Chen, J, Lu, J, Song, J.
Deposit date:2023-06-03
Release date:2023-11-22
Last modified:2025-07-30
Method:X-RAY DIFFRACTION (2.91 Å)
Cite:DNA conformational dynamics in the context-dependent non-CG CHH methylation by plant methyltransferase DRM2.
J.Biol.Chem., 299, 2023
8T9C
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BU of 8t9c by Molmil
Zophobas morio black wasting virus strain UT-morio virion structure
Descriptor: DNA (5'-D(P*CP*AP*GP*GP*CP*CP*AP*A)-3'), DNA (5'-D(P*CP*G)-3'), DNA (5'-D(P*CP*GP*A)-3'), ...
Authors:Penzes, J.J, Kaelber, J.T.
Deposit date:2023-06-23
Release date:2023-08-23
Last modified:2025-07-30
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:Cryo-EM-based discovery of a pathogenic parvovirus causing epidemic mortality by black wasting disease in farmed beetles.
Cell, 187, 2024
8T9E
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BU of 8t9e by Molmil
Zophobas morio black wasting virus strain UT-morio empty capsid structure
Descriptor: Major capsid protein
Authors:Penzes, J.J, Kaelber, J.T.
Deposit date:2023-06-23
Release date:2023-08-02
Last modified:2025-07-30
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Cryo-EM-based discovery of a pathogenic parvovirus causing epidemic mortality by black wasting disease in farmed beetles.
Cell, 187, 2024
8T9X
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BU of 8t9x by Molmil
Zophobas morio black wasting virus strain NJ2-molitor virion structure
Descriptor: DNA (5'-D(P*CP*AP*GP*GP*CP*CP*AP*AP*A)-3'), DNA (5'-D(P*CP*GP*A)-3'), DNA (5'-D(P*TP*CP*GP*AP*A)-3'), ...
Authors:Penzes, J.J, Kaelber, J.T.
Deposit date:2023-06-26
Release date:2024-02-21
Last modified:2025-07-30
Method:ELECTRON MICROSCOPY (2 Å)
Cite:Cryo-EM-based discovery of a pathogenic parvovirus causing epidemic mortality by black wasting disease in farmed beetles.
Cell, 187, 2024
8TA7
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BU of 8ta7 by Molmil
Zophobas morio black wasting virus strain OR-molitor empty capsid structure
Descriptor: Major capsid protein
Authors:Penzes, J.J, Kaelber, J.T.
Deposit date:2023-06-26
Release date:2023-08-02
Last modified:2025-07-30
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:Cryo-EM-based discovery of a pathogenic parvovirus causing epidemic mortality by black wasting disease in farmed beetles.
Cell, 187, 2024
8TJE
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BU of 8tje by Molmil
Zophobas morio black wasting virus strain OR-molitor virion structure
Descriptor: DNA (5'-D(P*CP*AP*GP*GP*CP*CP*AP*AP*A)-3'), DNA (5'-D(P*CP*G)-3'), DNA (5'-D(P*TP*CP*GP*AP*A)-3'), ...
Authors:Penzes, J.J, Kaelber, J.T.
Deposit date:2023-07-20
Release date:2023-08-23
Last modified:2025-07-30
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Cryo-EM-based discovery of a pathogenic parvovirus causing epidemic mortality by black wasting disease in farmed beetles.
Cell, 187, 2024
8UBS
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BU of 8ubs by Molmil
Crystal structure of NrdJ-1 split intein fusion
Descriptor: FORMIC ACID, NrdJ-1, SODIUM ION
Authors:Kofoed, C, Ye, X, Jeffrey, P.D, Muir, T.W.
Deposit date:2023-09-24
Release date:2024-10-09
Last modified:2025-07-30
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Programmable protein ligation on cell surfaces
Nature, 2025
8UUI
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BU of 8uui by Molmil
X-ray structure of Interleukin-23 in complex with peptide 23-446
Descriptor: Interleukin-12 subunit beta, Interleukin-23 subunit alpha, alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Joseph, J.S, Sridhar, V.S, Liu, M, Hu, Y, Gatchalian, J.
Deposit date:2023-11-01
Release date:2025-07-09
Last modified:2025-07-30
Method:X-RAY DIFFRACTION (2.43 Å)
Cite:Identification of an Induced Orthosteric Pocket in IL-23: A New Avenue for Non-biological Therapeutic Targeting.
Acs Chem.Biol., 20, 2025
8VAW
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BU of 8vaw by Molmil
Magnesium catalyzed primer extension product with 14mer primer and mixed phosphorothioate activated G monomer
Descriptor: 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE, MAGNESIUM ION, Magnesium catalyzed nonenzymatic RNA primer extension product
Authors:Fang, Z, Szostak, J.W.
Deposit date:2023-12-11
Release date:2024-04-17
Last modified:2025-07-30
Method:X-RAY DIFFRACTION (1.25 Å)
Cite:Catalytic Metal Ion-Substrate Coordination during Nonenzymatic RNA Primer Extension.
J.Am.Chem.Soc., 146, 2024
8VAX
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BU of 8vax by Molmil
Cadmium catalyzed primer extension product with 14mer primer and mixed phosphorothioate activated G monomer
Descriptor: 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE, Cadmium catalyzed nonenzymatic RNA primer extension product, MAGNESIUM ION
Authors:Fang, Z, Szostak, J.W.
Deposit date:2023-12-11
Release date:2024-04-17
Last modified:2025-07-30
Method:X-RAY DIFFRACTION (1.417 Å)
Cite:Catalytic Metal Ion-Substrate Coordination during Nonenzymatic RNA Primer Extension.
J.Am.Chem.Soc., 146, 2024
8VK6
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BU of 8vk6 by Molmil
14alpha-demethylase (CYP51) with amide-linked long arm extension antifungal azole inhibitor
Descriptor: DODECYL-BETA-D-MALTOSIDE, Lanosterol 14-alpha demethylase, N-[(2S)-2-(2,4-difluorophenyl)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]-4'-(trifluoromethoxy)[1,1'-biphenyl]-4-carboxamide, ...
Authors:Tyndall, J.D.A, Monk, B.C, Simons, C.
Deposit date:2024-01-08
Release date:2025-01-15
Last modified:2025-07-30
Method:X-RAY DIFFRACTION (1.89 Å)
Cite:Exploring Long Arm Amide-Linked Side Chains in the Design of Antifungal Azole Inhibitors of Sterol 14 alpha-Demethylase (CYP51).
J.Med.Chem., 68, 2025
8VWE
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BU of 8vwe by Molmil
HIV-1 neutralizing antibody D5_AR bound to HIV-1 gp41 coiled-coil pocket IQN17
Descriptor: Neutralizing antibody D5_AR Heavy Chain, Neutralizing antibody D5_AR Light Chain, Transmembrane protein gp41 IQN17 peptide
Authors:Filsinger Interrante, M.V, Tang, S, Fernandez, D, Kim, P.S.
Deposit date:2024-02-01
Release date:2025-07-02
Last modified:2025-07-30
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Utilizing Machine Learning to Improve Neutralization Potency of an HIV-1 Antibody Targeting the gp41 N-Heptad Repeat.
Acs Chem.Biol., 20, 2025
8VYA
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BU of 8vya by Molmil
SARS-CoV-2 Omicron Variant Spike Glycoprotein Fusion Core (Q954H)
Descriptor: SARS-CoV-2 Omicron variant spike glycoprotein C-terminal heptad repeat domain, SARS-CoV-2 Omicron variant spike glycoprotein N-terminal heptad repeat domain (Q954H)
Authors:Outlaw, V.K, Apurba, R, Vithanage, N.
Deposit date:2024-02-07
Release date:2025-02-19
Last modified:2025-07-30
Method:X-RAY DIFFRACTION (2.12 Å)
Cite:SARS-CoV-2 Omicron Variant Spike Glycoprotein Mutation Q954H Enhances Fusion Core Stability.
Acs Chem.Biol., 20, 2025
8WYH
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BU of 8wyh by Molmil
The global map of Omicron Subvariants Spike with ACE2
Descriptor: Angiotensin-converting enzyme 2, Spike glycoprotein
Authors:Yan, R.H, Wang, A.J, Yang, H.N.
Deposit date:2023-10-31
Release date:2024-11-13
Last modified:2025-07-30
Method:ELECTRON MICROSCOPY (3 Å)
Cite:Structural basis for the evolution and antibody evasion of SARS-CoV-2 BA.2.86 and JN.1 subvariants.
Nat Commun, 15, 2024
8WYJ
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BU of 8wyj by Molmil
The global map of Omicron Subvariants Spike with two antibodies
Descriptor: S309-HC, S309-KC, SA55-HC, ...
Authors:Yan, R.H, Wang, A.J, Yang, H.N.
Deposit date:2023-10-31
Release date:2024-11-13
Last modified:2025-07-30
Method:ELECTRON MICROSCOPY (3.1 Å)
Cite:Structural basis for the evolution and antibody evasion of SARS-CoV-2 BA.2.86 and JN.1 subvariants.
Nat Commun, 15, 2024
8XMK
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BU of 8xmk by Molmil
Local refinement of SRCR5-9 domains
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, Scavenger receptor cysteine-rich type 1 protein M130
Authors:Xu, H, Su, X.D.
Deposit date:2023-12-27
Release date:2025-01-01
Last modified:2025-07-30
Method:ELECTRON MICROSCOPY (3.03 Å)
Cite:Calcium-dependent oligomerization of scavenger receptor CD163 facilitates the endocytosis of ligands
Nat Commun, 16, 2025
8XMP
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BU of 8xmp by Molmil
Structure of CD163 in complex with Hb-Hp
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:Xu, H, Su, X.D.
Deposit date:2023-12-27
Release date:2025-01-01
Last modified:2025-07-30
Method:ELECTRON MICROSCOPY (3.11 Å)
Cite:Calcium-dependent oligomerization of scavenger receptor CD163 facilitates the endocytosis of ligands
Nat Commun, 16, 2025
8XMQ
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Structure of dimeric CD163 in complex with Hb-Hp
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:Xu, H, Su, X.D.
Deposit date:2023-12-27
Release date:2025-01-01
Last modified:2025-07-30
Method:ELECTRON MICROSCOPY (3.21 Å)
Cite:Calcium-dependent oligomerization of scavenger receptor CD163 facilitates the endocytosis of ligands
Nat Commun, 16, 2025
8XMW
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BU of 8xmw by Molmil
Local refinement of Hb-Hp bind to CD163
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:Xu, H, Su, X.D.
Deposit date:2023-12-28
Release date:2025-01-01
Last modified:2025-07-30
Method:ELECTRON MICROSCOPY (2.94 Å)
Cite:Calcium-dependent oligomerization of scavenger receptor CD163 facilitates the endocytosis of ligands
Nat Commun, 16, 2025
8XP6
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BU of 8xp6 by Molmil
2OG-Fe(II) oxygenase-ColD
Descriptor: 2OG-Fe(II) oxygenase, FE (III) ION
Authors:Zhang, B, Shi, J, Zhang, Y, Ge, H.M.
Deposit date:2024-01-03
Release date:2025-01-15
Last modified:2025-07-30
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Biosynthesis of Collinodin Unveils Iterative Oxidative and Prenylation Modifications
Acs Catalysis, 15, 2025
8XPF
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2OG-Fe(II) oxygenase-ColD in complex with collinodins
Descriptor: 2-OXOGLUTARIC ACID, 2OG-Fe(II) oxygenase, FE (III) ION, ...
Authors:Zhang, B, Shi, J, Zhang, Y, Ge, H.M.
Deposit date:2024-01-03
Release date:2025-01-15
Last modified:2025-07-30
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Biosynthesis of Collinodin Unveils Iterative Oxidative and Prenylation Modifications
Acs Catalysis, 15, 2025

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PDB entries from 2025-07-30

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