5cuc

Crystal structure of the bromodomain of bromodomain adjacent to zinc finger domain protein 2B (BAZ2B) in complex with N-Acetyl-2-phenylethylamine (SGC - Diamond I04-1 fragment screening)

Method: X-RAY DIFFRACTION Dmax: 63.2 Å Quality: GOOD

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

Bromodomain adjacent to zinc finger domain protein 2B

Homo sapiens

UniProt Q9UIF8

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 1858–1970 Fragment:Bromodomain, UNP residues 1858-1970 54W N-(2-phenylethyl)acetamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;277 K;20% PEG6000, 10% ethylene glycol, 0.1M MES pH 6.0, 0.1M calcium chloride Resolution 1.85 Å R-free 0.230

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.

263 other PDB entries and 271 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BAZ2B_HUMAN
Isoform Q9UIF8-4
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–115; UniProt 1858–1970

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 5cuc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5cuc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5cuc
Deposition date deposition_date2015-07-24
Structure title titleCrystal structure of the bromodomain of bromodomain adjacent to zinc finger domain protein 2B (BAZ2B) in complex with N-Acetyl-2-phenylethylamine (SGC - Diamond I04-1 fragment screening)
Keywords keywordsStructural Genomics, Structural Genomics Consortium, SGC, transcription; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier16.75
Radius of gyration Rg (electron density) rg_electron16.02
Forward intensity I(0) i03552690.00
Molecular weight molecular_weight13470.0 kDa
Excluded volume excluded_volume16934 ų
Envelope volume envelope_volume20826 ų
Hydration-shell volume shell_volume11783 ų
Envelope diameter envelope_diameter62.6
Shell Rg shell_rg21.08
Envelope Rg envelope_rg17.25
Shape Rg shape_rg15.93
Total Rg total_rg17.32
Total atoms total_atoms946
Residues n_residues115
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 dmax63.2
Rg (real space) rg_real16.91
Rg uncertainty (real space) rg_real_error0.57
I(0) (real space) i0_real3.5530e+06
I(0) uncertainty (real space) i0_real_error5.1540e+04
Rg (reciprocal space) rg_reciprocal16.89
I(0) (reciprocal space) i0_reciprocal3553000.0000
Solution quality estimate total_estimate0.7763
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary62.4
Skewness Skewness skewness0.701
Kurtosis Kurtosis kurtosis0.451
Angular range angular_range— – 0.4750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha614100.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.476; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.729; Smooth: 0.931

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5cuca1
Class classa — All alpha proteins
Fold Fold folda.29 — Bromodomain-like
Superfamily Superfamily superfamilya.29.2 — Bromodomain
Family Family familya.29.2.0 — automated matches
Domain ID domain_idd5cuca2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id5cucA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily10 — Bromodomain-like

8. Citations (1)

9. Files and Curves (10)