1kcq

Human Gelsolin Domain 2 with a Cd2+ bound

Method: X-RAY DIFFRACTION Dmax: 46.9 Å Quality: GOOD

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

GELSOLIN

Homo sapiens

UniProt P06396

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 185–288 Fragment:DOMAIN 2 CD CADMIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;290 K;PEG 400, cadmium chloride, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP at 290K Resolution 1.65 Å R-free 0.233
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 185–288 Fragment:DOMAIN 2 CD CADMIUM ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;290 K;PEG 400, cadmium chloride, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP at 290K Resolution 1.65 Å R-free 0.233

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.

60 other PDB entries and 93 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GELS_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–104; UniProt 185–288

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 1kcq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1kcq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1kcq
Deposition date deposition_date2001-11-09
Structure title titleHuman Gelsolin Domain 2 with a Cd2+ bound
Keywords keywordsalpha-beta structure, actin-binding protein, familial amyloidosis--Finnish type, cadmium binding, metal binding, structural protein; STRUCTURAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier14.13
Radius of gyration Rg (electron density) rg_electron12.85
Forward intensity I(0) i03389140.00
Molecular weight molecular_weight11730.0 kDa
Excluded volume excluded_volume14055 ų
Envelope volume envelope_volume15756 ų
Hydration-shell volume shell_volume10531 ų
Envelope diameter envelope_diameter46.4
Shell Rg shell_rg18.49
Envelope Rg envelope_rg13.32
Shape Rg shape_rg12.80
Total Rg total_rg14.12
Total atoms total_atoms798
Residues n_residues104
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 dmax46.9
Rg (real space) rg_real14.05
Rg uncertainty (real space) rg_real_error0.37
I(0) (real space) i0_real3.3890e+06
I(0) uncertainty (real space) i0_real_error4.0250e+04
Rg (reciprocal space) rg_reciprocal14.05
I(0) (reciprocal space) i0_reciprocal3389000.0000
Solution quality estimate total_estimate0.8849
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.8
Skewness Skewness skewness0.163
Kurtosis Kurtosis kurtosis-0.390
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha487600.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.980

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1kcqa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.109 — Gelsolin-like
Superfamily Superfamily superfamilyd.109.1 — Actin depolymerizing proteins
Family Family familyd.109.1.1 — Gelsolin-like

CATH v4.4 (1 domains)

Domain ID domain_id1kcqA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology20 — Severin
Homologous superfamily homologous superfamily10 — Severin

8. Citations (1)

9. Files and Curves (10)