1gyk

Serum Amyloid P Component co-crystallised with MOBDG at neutral pH

Method: X-RAY DIFFRACTION Dmax: 102.3 Å Quality: REASONABLE

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

SERUM AMYLOID P-COMPONENT

OrganismNot specified

UniProt P02743

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 20–223 Chain B; UniProt 20–223 Chain C; UniProt 20–223 Chain D; UniProt 20–223 Chain E; UniProt 20–223 Not recorded CA CALCIUM ION × 9 CDG METHYL 4,6-O-[(1R)-1-CARBOXYETHYLIDENE]-BETA-D-GALACTOPYRANOSIDE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8;pH 8.00 Resolution 2.20 Å R-free 0.224

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.

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

View Construct and Data Evidence
UniProt name SAMP_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–204; UniProt 20–223 Author chain B; PDBConstruct 1–204; UniProt 20–223 Author chain C; PDBConstruct 1–204; UniProt 20–223 Author chain D; PDBConstruct 1–204; UniProt 20–223 Author chain E; PDBConstruct 1–204; UniProt 20–223

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 1gyk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1gyk
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id1gyk
Deposition date deposition_date2002-04-25
Structure title titleSerum Amyloid P Component co-crystallised with MOBDG at neutral pH
Keywords keywordsPENTRAXIN, AMYLOID LECTIN, GLYCOPROTEIN, PLASMA, POLYMORPHISM; GLYCOPROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier36.49
Radius of gyration Rg (electron density) rg_electron35.30
Forward intensity I(0) i0192314000.00
Molecular weight molecular_weight117700.0 kDa
Excluded volume excluded_volume149290 ų
Envelope volume envelope_volume189050 ų
Hydration-shell volume shell_volume42648 ų
Envelope diameter envelope_diameter106.3
Shell Rg shell_rg44.21
Envelope Rg envelope_rg34.34
Shape Rg shape_rg35.30
Total Rg total_rg35.94
Total atoms total_atoms8326
Residues n_residues1020
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 dmax102.3
Rg (real space) rg_real36.30
Rg uncertainty (real space) rg_real_error0.68
I(0) (real space) i0_real1.9230e+08
I(0) uncertainty (real space) i0_real_error3.0170e+06
Rg (reciprocal space) rg_reciprocal36.42
I(0) (reciprocal space) i0_reciprocal192300000.0000
Solution quality estimate total_estimate0.6336
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary54.7
Skewness Skewness skewness-0.012
Kurtosis Kurtosis kurtosis-0.843
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha152200000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.980; Stabil: 1.000; Sysdev: 0.048; Positv: 1.000; Valcen: 0.998; Smooth: 0.152

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd1gyka_
Class classb — All beta proteins
Fold Fold foldb.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamilyb.29.1 — Concanavalin A-like lectins/glucanases
Family Family familyb.29.1.5 — Pentraxin (pentaxin)
Domain ID domain_idd1gykb_
Class classb — All beta proteins
Fold Fold foldb.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamilyb.29.1 — Concanavalin A-like lectins/glucanases
Family Family familyb.29.1.5 — Pentraxin (pentaxin)
Domain ID domain_idd1gykc_
Class classb — All beta proteins
Fold Fold foldb.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamilyb.29.1 — Concanavalin A-like lectins/glucanases
Family Family familyb.29.1.5 — Pentraxin (pentaxin)
Domain ID domain_idd1gykd_
Class classb — All beta proteins
Fold Fold foldb.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamilyb.29.1 — Concanavalin A-like lectins/glucanases
Family Family familyb.29.1.5 — Pentraxin (pentaxin)
Domain ID domain_idd1gyke_
Class classb — All beta proteins
Fold Fold foldb.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamilyb.29.1 — Concanavalin A-like lectins/glucanases
Family Family familyb.29.1.5 — Pentraxin (pentaxin)

CATH v4.4 (5 domains)

Domain ID domain_id1gykA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200
Domain ID domain_id1gykB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200
Domain ID domain_id1gykC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200
Domain ID domain_id1gykD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200
Domain ID domain_id1gykE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200

8. Citations (1)

9. Files and Curves (10)