5urc

Design, Synthesis, Functional and Biological Evaluation of Ether and Ester Derivatives of the Antisickling Agent 5-HMF for the Treatment of Sickle Cell Disease

Method: X-RAY DIFFRACTION Dmax: 81.4 Å Quality: GOOD

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

Hemoglobin subunit alpha

OrganismNot specified

UniProt P69905

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 2–142 Chain C; UniProt 2–142 Not recorded Hemoglobin subunit beta × 2 (P68871) CMO CARBON MONOXIDE × 4 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 8MV (5-formylfuran-2-yl)methyl acetate × 1 FUX 5-HYDROXYMETHYL-FURFURAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH MODE;pH 7.4;298 K;25% PEG4000, 0.1 M Hepes, 40 mM Sodium Chloride Resolution 1.85 Å R-free 0.223

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.

348 other PDB entries and 412 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HBA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–141; UniProt 2–142 Author chain C; PDBConstruct 1–141; UniProt 2–142

Hemoglobin subunit beta

OrganismNot specified

UniProt P68871

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 2–147 Chain D; UniProt 2–147 Not recorded Hemoglobin subunit alpha × 2 (P69905) CMO CARBON MONOXIDE × 4 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 8MV (5-formylfuran-2-yl)methyl acetate × 1 FUX 5-HYDROXYMETHYL-FURFURAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH MODE;pH 7.4;298 K;25% PEG4000, 0.1 M Hepes, 40 mM Sodium Chloride Resolution 1.85 Å R-free 0.223

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.

343 other PDB entries and 399 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HBB_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–146; UniProt 2–147 Author chain D; PDBConstruct 1–146; UniProt 2–147

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 5urc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5urc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5urc
Deposition date deposition_date2017-02-10
Structure title titleDesign, Synthesis, Functional and Biological Evaluation of Ether and Ester Derivatives of the Antisickling Agent 5-HMF for the Treatment of Sickle Cell Disease
Keywords keywordshemoglobin, antisickling, allosteric effector, aromatic aldehyde, OXYGEN TRANSPORT; OXYGEN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.56
Radius of gyration Rg (electron density) rg_electron23.30
Forward intensity I(0) i064032900.00
Molecular weight molecular_weight64830.0 kDa
Excluded volume excluded_volume82010 ų
Envelope volume envelope_volume95072 ų
Hydration-shell volume shell_volume32661 ų
Envelope diameter envelope_diameter72.4
Shell Rg shell_rg31.37
Envelope Rg envelope_rg23.13
Shape Rg shape_rg23.28
Total Rg total_rg24.23
Total atoms total_atoms4583
Residues n_residues574
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 dmax81.4
Rg (real space) rg_real24.33
Rg uncertainty (real space) rg_real_error0.42
I(0) (real space) i0_real6.4030e+07
I(0) uncertainty (real space) i0_real_error8.3920e+05
Rg (reciprocal space) rg_reciprocal24.38
I(0) (reciprocal space) i0_reciprocal64040000.0000
Solution quality estimate total_estimate0.7954
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary32.3
Skewness Skewness skewness0.045
Kurtosis Kurtosis kurtosis-0.534
Angular range angular_range— – 0.3250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha20490000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.780; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5urca_
Class classa — All alpha proteins
Fold Fold folda.1 — Globin-like
Superfamily Superfamily superfamilya.1.1 — Globin-like
Family Family familya.1.1.2 — Globins
Domain ID domain_idd5urcb_
Class classa — All alpha proteins
Fold Fold folda.1 — Globin-like
Superfamily Superfamily superfamilya.1.1 — Globin-like
Family Family familya.1.1.2 — Globins
Domain ID domain_idd5urcc_
Class classa — All alpha proteins
Fold Fold folda.1 — Globin-like
Superfamily Superfamily superfamilya.1.1 — Globin-like
Family Family familya.1.1.2 — Globins
Domain ID domain_idd5urcd_
Class classa — All alpha proteins
Fold Fold folda.1 — Globin-like
Superfamily Superfamily superfamilya.1.1 — Globin-like
Family Family familya.1.1.2 — Globins

CATH v4.4 (4 domains)

Domain ID domain_id5urcA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5urcB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5urcC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5urcD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins

8. Citations (1)

9. Files and Curves (10)