5ptc

PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 156)

Method: X-RAY DIFFRACTION Dmax: 67.9 Å Quality: EXCELLENT

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

Bromodomain-containing protein 1

Homo sapiens

UniProt O95696

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 555–688 Mutation:V23M,P34E,V37R EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;0.1M bis-tris pH 7.0 -- 30% PEG3350 Resolution 1.78 Å R-free 0.221
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 555–688 Mutation:V23M,P34E,V37R EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;293 K;0.1M bis-tris pH 7.0 -- 30% PEG3350 Resolution 1.78 Å R-free 0.221

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.

309 other PDB entries and 621 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BRD1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 23–156; UniProt 555–688 Author chain B; PDBConstruct 23–156; UniProt 555–688

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 5ptc

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5ptc
Deposition date deposition_date2017-02-07
Structure title titlePanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 156)
Keywords keywordsPanDDA, SGC - Diamond I04-1 fragment screening, bromodomain, epigenetics, XChemExplorer, GENE REGULATION; GENE REGULATION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.73
Radius of gyration Rg (electron density) rg_electron20.77
Forward intensity I(0) i014415900.00
Molecular weight molecular_weight28013.0 kDa
Excluded volume excluded_volume34773 ų
Envelope volume envelope_volume44175 ų
Hydration-shell volume shell_volume18059 ų
Envelope diameter envelope_diameter68.4
Shell Rg shell_rg26.93
Envelope Rg envelope_rg20.89
Shape Rg shape_rg20.72
Total Rg total_rg21.77
Total atoms total_atoms1966
Residues n_residues244
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 dmax67.9
Rg (real space) rg_real21.67
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real1.4420e+07
I(0) uncertainty (real space) i0_real_error2.0470e+05
Rg (reciprocal space) rg_reciprocal21.68
I(0) (reciprocal space) i0_reciprocal14420000.0000
Solution quality estimate total_estimate0.9048
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.3
Skewness Skewness skewness0.172
Kurtosis Kurtosis kurtosis-0.626
Angular range angular_range— – 0.3650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4043000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.990

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id5ptcA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily10 — Bromodomain-like
Domain ID domain_id5ptcB00
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)