6g5p

Crystal structure of human SP100 in complex with bromodomain-focused fragment FM009493b 2,3-Dimethoxy-2,3-dimethyl-2,3-dihydro-1,4-benzodioxin-6-amine

Method: X-RAY DIFFRACTION Dmax: 80.2 Å Quality: EXCELLENT

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

Nuclear autoantigen Sp-100

Homo sapiens

UniProt P23497

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 700–879 Not recorded ZN ZINC ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 EDO 1,2-ETHANEDIOL × 3 EN8 (2~{R},3~{R})-2,3-dimethoxy-2,3-dimethyl-1,4-benzodioxin-6-amine × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.1;277 K;17-23% PEG20K, 0.1M MES 6.1, 2-4% Ethylene glycol, 4 days Resolution 1.35 Å R-free 0.174
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 700–879 Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.1;277 K;17-23% PEG20K, 0.1M MES 6.1, 2-4% Ethylene glycol, 4 days Resolution 1.35 Å R-free 0.174

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.

122 other PDB entries and 241 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SP100_HUMAN
Isoform P23497-4
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–180; UniProt 700–879 Author chain B; PDBConstruct 1–180; UniProt 700–879

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 6g5p

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6g5p
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6g5p
Deposition date deposition_date2018-03-29
Structure title titleCrystal structure of human SP100 in complex with bromodomain-focused fragment FM009493b 2,3-Dimethoxy-2,3-dimethyl-2,3-dihydro-1,4-benzodioxin-6-amine
Keywords keywords;FRAGMENT SCREENING, EPIGENETICS, BROMODOMAIN, STRUCTURAL GENOMICS CONSORTIUM, SGC, XCHEM, DIAMOND I04-1, PANDDA, XCHEMEXPLORER, TRANSCRIPTION ;; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.46
Radius of gyration Rg (electron density) rg_electron24.44
Forward intensity I(0) i032335800.00
Molecular weight molecular_weight42010.0 kDa
Excluded volume excluded_volume51779 ų
Envelope volume envelope_volume65539 ų
Hydration-shell volume shell_volume22993 ų
Envelope diameter envelope_diameter82.7
Shell Rg shell_rg30.74
Envelope Rg envelope_rg24.44
Shape Rg shape_rg24.41
Total Rg total_rg25.28
Total atoms total_atoms2930
Residues n_residues348
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 dmax80.2
Rg (real space) rg_real25.46
Rg uncertainty (real space) rg_real_error0.56
I(0) (real space) i0_real3.2340e+07
I(0) uncertainty (real space) i0_real_error4.6830e+05
Rg (reciprocal space) rg_reciprocal25.46
I(0) (reciprocal space) i0_reciprocal32340000.0000
Solution quality estimate total_estimate0.9086
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.4
Skewness Skewness skewness0.282
Kurtosis Kurtosis kurtosis-0.592
Angular range angular_range— – 0.3100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3185000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.984

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id6g5pA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
Domain ID domain_id6g5pA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily10 — Bromodomain-like
Domain ID domain_id6g5pB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
Domain ID domain_id6g5pB02
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)