6fnb

Mono- and bivalent 14-3-3 inhibitors for characterizing supramolecular lysine-PEG interactions in proteins

Method: X-RAY DIFFRACTION Dmax: 84.2 Å Quality: EXCELLENT

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

14-3-3 protein zeta/delta

Homo sapiens

UniProt P63104

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–230 Chain B; UniProt 1–230 Not recorded BEZ BENZOIC ACID × 2 GOL GLYCEROL × 3 CA CALCIUM ION × 2 CL CHLORIDE ION × 4 DWQ [2-[2-oxidanylidene-2-[[3-[2-[5-[3-oxidanylidene-3-[3-[2-[2-[3-[3-[2-[2-[2-[[3-[2-(2-phosphonophenoxy)ethanoylamino]phenyl]carbonylamino]ethoxy]ethoxy]ethoxy]propanoylamino]propoxy]ethoxy]ethoxy]propylamino]propoxy]pentoxy]ethylcarbamoyl]phenyl]amino]ethoxy]phenyl]phosphonic acid × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277.15 K;0.09 M HEPES sodium salt pH 7.5 1.26 M tri-Sodium citrate 10 %(v/v) Glycerol Resolution 2.30 Å R-free 0.248

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.

73 other PDB entries and 88 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1433Z_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–230; UniProt 1–230 Author chain B; PDBConstruct 1–230; UniProt 1–230

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 6fnb

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6fnb
Deposition date deposition_date2018-02-02
Structure title titleMono- and bivalent 14-3-3 inhibitors for characterizing supramolecular lysine-PEG interactions in proteins
Keywords keywordsInhibition, Mono- and bivalent 14-3-3 inhibitors, Supramolecular lysine-PEG, protein binding; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.16
Radius of gyration Rg (electron density) rg_electron26.41
Forward intensity I(0) i046234900.00
Molecular weight molecular_weight52172.0 kDa
Excluded volume excluded_volume64955 ų
Envelope volume envelope_volume83881 ų
Hydration-shell volume shell_volume26549 ų
Envelope diameter envelope_diameter85.3
Shell Rg shell_rg33.66
Envelope Rg envelope_rg25.99
Shape Rg shape_rg26.46
Total Rg total_rg27.06
Total atoms total_atoms3654
Residues n_residues457
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 dmax84.2
Rg (real space) rg_real27.12
Rg uncertainty (real space) rg_real_error0.62
I(0) (real space) i0_real4.6230e+07
I(0) uncertainty (real space) i0_real_error7.3350e+05
Rg (reciprocal space) rg_reciprocal27.14
I(0) (reciprocal space) i0_reciprocal46240000.0000
Solution quality estimate total_estimate0.9102
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary30.5
Skewness Skewness skewness0.215
Kurtosis Kurtosis kurtosis-0.676
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7764000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.932

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6fnba_
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.7 — 14-3-3 protein
Family Family familya.118.7.1 — 14-3-3 protein
Domain ID domain_idd6fnbb_
Class classa — All alpha proteins
Fold Fold folda.118 — alpha-alpha superhelix
Superfamily Superfamily superfamilya.118.7 — 14-3-3 protein
Family Family familya.118.7.1 — 14-3-3 protein

CATH v4.4 (2 domains)

Domain ID domain_id6fnbA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology190 — Delta-Endotoxin; domain 1
Homologous superfamily homologous superfamily20 — 14-3-3 domain
Domain ID domain_id6fnbB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology190 — Delta-Endotoxin; domain 1
Homologous superfamily homologous superfamily20 — 14-3-3 domain

8. Citations (1)

9. Files and Curves (10)