6zyf

Notum_Ghrelin complex

Method: X-RAY DIFFRACTION Dmax: 99.2 Å Quality: GOOD

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

Palmitoleoyl-protein carboxylesterase NOTUM

Homo sapiens

UniProt Q6P988

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 81–451 Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 K4Q [(2~{S})-2-azanyl-3-oxidanylidene-propyl] octanoate × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;pH 7;296 K;0.1 M Hepes pH 7.0 0.1 M KCl 15% PEG MME 5000 Resolution 2.19 Å R-free 0.252
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 81–451 Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 K4Q [(2~{S})-2-azanyl-3-oxidanylidene-propyl] octanoate × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;pH 7;296 K;0.1 M Hepes pH 7.0 0.1 M KCl 15% PEG MME 5000 Resolution 2.19 Å R-free 0.252

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.

140 other PDB entries and 148 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NOTUM_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–374; UniProt 81–451 Author chain B; PDBConstruct 4–374; UniProt 81–451

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 6zyf

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6zyf
Deposition date deposition_date2020-07-31
Structure title titleNotum_Ghrelin complex
Keywords keywordsNotum Ghrelin, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.33
Radius of gyration Rg (electron density) rg_electron30.60
Forward intensity I(0) i0106948000.00
Molecular weight molecular_weight80595.0 kDa
Excluded volume excluded_volume100190 ų
Envelope volume envelope_volume128800 ų
Hydration-shell volume shell_volume34769 ų
Envelope diameter envelope_diameter96.6
Shell Rg shell_rg38.27
Envelope Rg envelope_rg30.11
Shape Rg shape_rg30.59
Total Rg total_rg31.30
Total atoms total_atoms5674
Residues n_residues701
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 dmax99.2
Rg (real space) rg_real31.33
Rg uncertainty (real space) rg_real_error0.73
I(0) (real space) i0_real1.0690e+08
I(0) uncertainty (real space) i0_real_error1.6280e+06
Rg (reciprocal space) rg_reciprocal31.33
I(0) (reciprocal space) i0_reciprocal106900000.0000
Solution quality estimate total_estimate0.8249
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.1
Skewness Skewness skewness0.251
Kurtosis Kurtosis kurtosis-0.729
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19200000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6zyfa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
Family Family familyc.69.1.42 — Pectinacetylesterase-like
Domain ID domain_idd6zyfb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
Family Family familyc.69.1.42 — Pectinacetylesterase-like

8. Citations (1)

9. Files and Curves (10)