4avt

Structure of CPHPC bound to Serum Amyloid P Component

Method: X-RAY DIFFRACTION Dmax: 114.4 Å Quality: GOOD

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 C; UniProt 20–223 Chain E; UniProt 20–223 Chain G; UniProt 20–223 Chain I; UniProt 20–223 Not recorded CA CALCIUM ION × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 GHE (2R)-1-[6-[(2R)-2-carboxypyrrolidin-1-yl]-6-oxidanylidene-hexanoyl]pyrrolidine-2-carboxylic acid × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.6;60MM TRIS-HCL, 80MM NACL, 15% PEG550 MME, pH 7.6 Resolution 3.20 Å R-free 0.197
2 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 20–223 Chain D; UniProt 20–223 Chain F; UniProt 20–223 Chain H; UniProt 20–223 Chain J; UniProt 20–223 Not recorded CA CALCIUM ION × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 GHE (2R)-1-[6-[(2R)-2-carboxypyrrolidin-1-yl]-6-oxidanylidene-hexanoyl]pyrrolidine-2-carboxylic acid × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.6;60MM TRIS-HCL, 80MM NACL, 15% PEG550 MME, pH 7.6 Resolution 3.20 Å R-free 0.197

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 13 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 Author chain F; PDBConstruct 1–204; UniProt 20–223 Author chain G; PDBConstruct 1–204; UniProt 20–223 Author chain H; PDBConstruct 1–204; UniProt 20–223 Author chain I; PDBConstruct 1–204; UniProt 20–223 Author chain J; 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 4avt

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4avt
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4avt
Deposition date deposition_date2012-05-29
Structure title titleStructure of CPHPC bound to Serum Amyloid P Component
Keywords keywordsSUGAR BINDING PROTEIN, LECTIN, METAL-BINDING; SUGAR BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier40.80
Radius of gyration Rg (electron density) rg_electron39.77
Forward intensity I(0) i0753405000.00
Molecular weight molecular_weight237110.0 kDa
Excluded volume excluded_volume300860 ų
Envelope volume envelope_volume392910 ų
Hydration-shell volume shell_volume78347 ų
Envelope diameter envelope_diameter119.8
Shell Rg shell_rg49.54
Envelope Rg envelope_rg38.17
Shape Rg shape_rg39.77
Total Rg total_rg40.28
Total atoms total_atoms16770
Residues n_residues2040
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 dmax114.4
Rg (real space) rg_real40.47
Rg uncertainty (real space) rg_real_error0.51
I(0) (real space) i0_real7.5340e+08
I(0) uncertainty (real space) i0_real_error1.2530e+07
Rg (reciprocal space) rg_reciprocal40.80
I(0) (reciprocal space) i0_reciprocal753700000.0000
Solution quality estimate total_estimate0.8289
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary58.7
Skewness Skewness skewness-0.146
Kurtosis Kurtosis kurtosis-0.609
Angular range angular_range— – 0.1950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha182600000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id4avtA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200
Domain ID domain_id4avtB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200
Domain ID domain_id4avtC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200
Domain ID domain_id4avtD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200
Domain ID domain_id4avtE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200
Domain ID domain_id4avtF00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200
Domain ID domain_id4avtG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200
Domain ID domain_id4avtH00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200
Domain ID domain_id4avtI00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200
Domain ID domain_id4avtJ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200

8. Citations (1)

9. Files and Curves (10)