6pdg

Crystal structure of MYST acetyltransferase domain in complex with inhibitor 83

Method: X-RAY DIFFRACTION Dmax: 80.9 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone acetyltransferase KAT8

Homo sapiens

UniProt Q9H7Z6

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 177–448 Mutation:A142S, L145M, T146I, K157R, W204S Non-standard monomer:Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 NA SODIUM ION × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 O9A 5-ethoxy-2-fluoro-3-methyl-N'-[(naphthalen-2-yl)sulfonyl]benzohydrazide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;292 K;27% PEG 3350, 0.2 M ammonium sulfate, 0.1 M bis-tris pH 6.5 Resolution 1.92 Å R-free 0.213

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.

41 other PDB entries and 44 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KAT8_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–272; UniProt 177–448

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 6pdg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6pdg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6pdg
Deposition date deposition_date2019-06-18
Structure title titleCrystal structure of MYST acetyltransferase domain in complex with inhibitor 83
Keywords keywordsInhibitor, Complex, MYST, TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.04
Radius of gyration Rg (electron density) rg_electron20.19
Forward intensity I(0) i016563500.00
Molecular weight molecular_weight31755.0 kDa
Excluded volume excluded_volume40091 ų
Envelope volume envelope_volume46116 ų
Hydration-shell volume shell_volume19780 ų
Envelope diameter envelope_diameter82.9
Shell Rg shell_rg26.25
Envelope Rg envelope_rg20.73
Shape Rg shape_rg20.16
Total Rg total_rg21.13
Total atoms total_atoms2235
Residues n_residues267
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax80.9
Rg (real space) rg_real21.09
Rg uncertainty (real space) rg_real_error0.85
I(0) (real space) i0_real1.6560e+07
I(0) uncertainty (real space) i0_real_error2.5150e+05
Rg (reciprocal space) rg_reciprocal21.08
I(0) (reciprocal space) i0_reciprocal16560000.0000
Solution quality estimate total_estimate0.7917
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.6
Skewness Skewness skewness0.494
Kurtosis Kurtosis kurtosis0.019
Angular range angular_range— – 0.3800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4060000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.489; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.823; Smooth: 0.999

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6pdga_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamilyd.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family familyd.108.1.0 — automated matches

8. Citations (1)

9. Files and Curves (10)