1waq

Crystal structure of human Growth and Differentiation Factor 5 (GDF-5)

Method: X-RAY DIFFRACTION Dmax: 69.8 Å Quality: GOOD

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

GROWTH/DIFFERENTIATION FACTOR 5

HOMO SAPIENS

UniProt P43026

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 387–501 Fragment:RESIDUES 387-501 (RESIDUES 6-120 OF MATURE GDF-5) MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 6 X-RAY DIFFRACTION X-ray crystallization conditions:25% 2-METHLY-2,4-PENTANEDIOL, 0.1M SODIUM CITRATE PH 4.0 Resolution 2.28 Å R-free 0.237

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.

14 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GDF5_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–117; UniProt 387–501

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 1waq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1waq
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id1waq
Deposition date deposition_date2004-10-27
Structure title titleCrystal structure of human Growth and Differentiation Factor 5 (GDF-5)
Keywords keywordsGROWTH FACTOR, TGF-BETA SUPERFAMILY, CYTOKINE; GROWTH FACTOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.18
Radius of gyration Rg (electron density) rg_electron19.21
Forward intensity I(0) i02961520.00
Molecular weight molecular_weight12183.0 kDa
Excluded volume excluded_volume15182 ų
Envelope volume envelope_volume19206 ų
Hydration-shell volume shell_volume9601 ų
Envelope diameter envelope_diameter68.4
Shell Rg shell_rg22.88
Envelope Rg envelope_rg19.56
Shape Rg shape_rg19.22
Total Rg total_rg19.84
Total atoms total_atoms849
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 dmax69.8
Rg (real space) rg_real19.51
Rg uncertainty (real space) rg_real_error0.56
I(0) (real space) i0_real2.9620e+06
I(0) uncertainty (real space) i0_real_error3.5850e+04
Rg (reciprocal space) rg_reciprocal19.46
I(0) (reciprocal space) i0_reciprocal2961000.0000
Solution quality estimate total_estimate0.7610
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.5
Skewness Skewness skewness0.569
Kurtosis Kurtosis kurtosis-0.400
Angular range angular_range— – 0.4150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha295800.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.577; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.209; Smooth: 0.951

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_idd1waqa_
Class classg — Small proteins
Fold Fold foldg.17 — Cystine-knot cytokines
Superfamily Superfamily superfamilyg.17.1 — Cystine-knot cytokines
Family Family familyg.17.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id1waqA00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily10 — Cystine-knot cytokines

8. Citations (2)

9. Files and Curves (10)