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7pw5

Human SMG1-8-9 kinase complex with AlphaFold predicted SMG8 C-terminus, bound to a SMG1 inhibitor

Method: ELECTRON MICROSCOPY Dmax: 186.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

;SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1 ;

Homo sapiens

UniProt Q96Q15

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 311–1638 Chain A； UniProt 1727–1978 Chain A； UniProt 2035–2056 Chain A； UniProt 2088–3661 Not recorded Protein SMG8 × 1 （Q8ND04） Protein SMG9 × 1 （Q9H0W8） IHP INOSITOL HEXAKISPHOSPHATE × 1 88C 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 3.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7PW5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6L53 Structure of SMG1 Deposited 2019-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–3661（3661 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.63 Å
6L54 Structure of SMG189 Deposited 2019-10-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–3661（3661 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.43 Å
6SYT Structure of the SMG1-SMG8-SMG9 complex Deposited 2019-10-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 311–1638（1328 aa）
Chain A 1727–1978（252 aa）
Chain A 2035–2056（22 aa）
Chain A 2088–2232（145 aa）
Chain A 2275–3661（1387 aa）
Mutation：D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A Mutation：D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A Mutation：D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A Mutation：D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A Mutation：D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A,D2335A IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；PBS
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.45 Å
6Z3R Structure of SMG1-8-9 kinase complex bound to UPF1-LSQ Deposited 2020-05-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 259–1638（1380 aa）
Chain A 1727–2056（330 aa）
Chain A 2088–3661（1574 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.97 Å
7PW4 Human SMG1-8-9 kinase complex bound to a SMG1 inhibitor Deposited 2021-10-06 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 311–1638（1328 aa）
Chain A 1727–1978（252 aa）
Chain A 2035–2056（22 aa）
Chain A 2088–3661（1574 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 88C 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.27 Å
7PW6 Human SMG1-8-9 kinase complex bound to a SMG1 inhibitor - SMG1 body Deposited 2021-10-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 766–1638（873 aa）
Chain A 1727–1978（252 aa）
Chain A 2035–2056（22 aa）
Chain A 2088–3661（1574 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 88C 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.05 Å
7PW7 Human SMG1-9 kinase complex bound to a SMG1 inhibitor Deposited 2021-10-06 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 311–1638（1328 aa）
Chain A 1727–1978（252 aa）
Chain A 2035–2056（22 aa）
Chain A 2088–3661（1574 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 88C 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.59 Å
7PW8 Human SMG1-8-9 kinase complex bound to AMPPNP Deposited 2021-10-06 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 311–1638（1328 aa）
Chain A 1727–1978（252 aa）
Chain A 1895–1916（22 aa）
Chain A 2088–3661（1574 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.82 Å
7PW9 Human SMG1-9 kinase complex bound to AMPPNP Deposited 2021-10-06 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 311–1638（1328 aa）
Chain A 1727–1978（252 aa）
Chain A 2035–2056（22 aa）
Chain A 2088–3661（1574 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.12 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SMG1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 307–1634； UniProt 311–1638 Author chain A； PDBConstruct 1723–1974； UniProt 1727–1978 Author chain A； PDBConstruct 2031–2052； UniProt 2035–2056 Author chain A； PDBConstruct 2084–3657； UniProt 2088–3661

Protein SMG8

Homo sapiens

UniProt Q8ND04

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 1–991 Not recorded ;SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1 ; × 1 （Q96Q15） Protein SMG9 × 1 （Q9H0W8） IHP INOSITOL HEXAKISPHOSPHATE × 1 88C 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 3.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7PW5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6L54 Structure of SMG189 Deposited 2019-10-22 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–991（991 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.43 Å
6SYT Structure of the SMG1-SMG8-SMG9 complex Deposited 2019-10-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–991（991 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；PBS
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.45 Å
6Z3R Structure of SMG1-8-9 kinase complex bound to UPF1-LSQ Deposited 2020-05-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–991（991 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.97 Å
7PW4 Human SMG1-8-9 kinase complex bound to a SMG1 inhibitor Deposited 2021-10-06 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–991（991 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 88C 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.27 Å
7PW8 Human SMG1-8-9 kinase complex bound to AMPPNP Deposited 2021-10-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–991（991 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.82 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SMG8_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–991； UniProt 1–991

Protein SMG9

Homo sapiens

UniProt Q9H0W8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 1–520 Not recorded ;SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1,SMG1,Serine/threonine-protein kinase SMG1 ; × 1 （Q96Q15） Protein SMG8 × 1 （Q8ND04） IHP INOSITOL HEXAKISPHOSPHATE × 1 88C 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE-PROPANE Resolution 3.40 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7PW5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6L54 Structure of SMG189 Deposited 2019-10-22 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–520（520 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.43 Å
6SYT Structure of the SMG1-SMG8-SMG9 complex Deposited 2019-10-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–520（520 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；PBS
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.45 Å
6Z3R Structure of SMG1-8-9 kinase complex bound to UPF1-LSQ Deposited 2020-05-21 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–520（520 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.97 Å
7PW4 Human SMG1-8-9 kinase complex bound to a SMG1 inhibitor Deposited 2021-10-06 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–520（520 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 88C 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.27 Å
7PW7 Human SMG1-9 kinase complex bound to a SMG1 inhibitor Deposited 2021-10-06 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–520（520 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 88C 1-[4-[4-[2-[[4-chloranyl-3-(diethylsulfamoyl)phenyl]amino]pyrimidin-4-yl]pyridin-2-yl]phenyl]-3-methyl-urea × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.59 Å
7PW8 Human SMG1-8-9 kinase complex bound to AMPPNP Deposited 2021-10-06 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–520（520 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.82 Å
7PW9 Human SMG1-9 kinase complex bound to AMPPNP Deposited 2021-10-06 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 169–520（352 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.12 Å
8FE7 Crystal structure of human O-GlcNAc transferase (OGT) in complex with an exosite-binding peptide (SMG9) and UDP-GlcNAc Deposited 2022-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 140–151（12 aa）
Not recorded UD1 URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.9M Ammonium Sulfate, 0.1M Tris pH 8.5, 1% Xylitol
Resolution 2.98 Å R-free 0.217
8FE7 Crystal structure of human O-GlcNAc transferase (OGT) in complex with an exosite-binding peptide (SMG9) and UDP-GlcNAc Deposited 2022-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 140–151（12 aa）
Not recorded UD1 URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.9M Ammonium Sulfate, 0.1M Tris pH 8.5, 1% Xylitol
Resolution 2.98 Å R-free 0.217
8FE7 Crystal structure of human O-GlcNAc transferase (OGT) in complex with an exosite-binding peptide (SMG9) and UDP-GlcNAc Deposited 2022-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 140–151（12 aa）
Not recorded UD1 URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.9M Ammonium Sulfate, 0.1M Tris pH 8.5, 1% Xylitol
Resolution 2.98 Å R-free 0.217
8FE7 Crystal structure of human O-GlcNAc transferase (OGT) in complex with an exosite-binding peptide (SMG9) and UDP-GlcNAc Deposited 2022-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 140–151（12 aa）
Not recorded UD1 URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.9M Ammonium Sulfate, 0.1M Tris pH 8.5, 1% Xylitol
Resolution 2.98 Å R-free 0.217

8 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SMG9_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–520； UniProt 1–520

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 7pw5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7pw5
Download Download
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7pw5
Deposition date deposition_date2021-10-06
Structure title titleHuman SMG1-8-9 kinase complex with AlphaFold predicted SMG8 C-terminus, bound to a SMG1 inhibitor
Keywords keywordsComplex, TRANSFERASE; TRANSFERASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier54.79 Å
Radius of gyration Rg (electron density) rg_electron54.16 Å
Forward intensity I(0) i01302790000.00
Molecular weight molecular_weight305490.0 kDa
Excluded volume excluded_volume384150 ų
Envelope volume envelope_volume632900 ų
Hydration-shell volume shell_volume96986 ų
Envelope diameter envelope_diameter204.3 Å
Shell Rg shell_rg56.97 Å
Envelope Rg envelope_rg54.05 Å
Shape Rg shape_rg54.21 Å
Total Rg total_rg54.05 Å
Total atoms total_atoms21548
Residues n_residues2956
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax186.2 Å
Rg (real space) rg_real54.76 Å
Rg uncertainty (real space) rg_real_error1.86 Å
I(0) (real space) i0_real1.3030e+09
I(0) uncertainty (real space) i0_real_error2.7160e+07
Rg (reciprocal space) rg_reciprocal54.80 Å
I(0) (reciprocal space) i0_reciprocal1303000000.0000
Solution quality estimate total_estimate0.8895
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary64.2 Å
Skewness Skewness skewness0.263
Kurtosis Kurtosis kurtosis-0.445
Angular range angular_range— – 0.1450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha101600000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.898
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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8. Citations (1)

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9. Files and Curves (10)