6xd9

Carbonmonoxy hemoglobin in complex with the antisickling agent 2-hydroxy-6-((6-(hydroxymethyl)pyridin-2-yl)methoxy)benzaldehyde (VZHE039)

Method: X-RAY DIFFRACTION Dmax: 71.2 Å Quality: EXCELLENT

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 V39 3-{[6-(hydroxymethyl)pyridin-2-yl]methoxy}-2-methylphenol × 2 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH MODE;pH 7.4;298 K;25% PEG 6000, 0.1M HEPES Resolution 2.10 Å R-free 0.258

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 V39 3-{[6-(hydroxymethyl)pyridin-2-yl]methoxy}-2-methylphenol × 2 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH MODE;pH 7.4;298 K;25% PEG 6000, 0.1M HEPES Resolution 2.10 Å R-free 0.258

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 6xd9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6xd9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6xd9
Deposition date deposition_date2020-06-10
Structure title titleCarbonmonoxy hemoglobin in complex with the antisickling agent 2-hydroxy-6-((6-(hydroxymethyl)pyridin-2-yl)methoxy)benzaldehyde (VZHE039)
Keywords keywordsHemoglobin, Aromatic aldehyde, Antisickling, Allosteric effector, 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_electron23.28
Forward intensity I(0) i064210800.00
Molecular weight molecular_weight65058.0 kDa
Excluded volume excluded_volume82336 ų
Envelope volume envelope_volume95551 ų
Hydration-shell volume shell_volume32806 ų
Envelope diameter envelope_diameter72.4
Shell Rg shell_rg31.43
Envelope Rg envelope_rg23.13
Shape Rg shape_rg23.26
Total Rg total_rg24.22
Total atoms total_atoms4600
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 dmax71.2
Rg (real space) rg_real24.33
Rg uncertainty (real space) rg_real_error0.25
I(0) (real space) i0_real6.4210e+07
I(0) uncertainty (real space) i0_real_error7.7020e+05
Rg (reciprocal space) rg_reciprocal24.38
I(0) (reciprocal space) i0_reciprocal64210000.0000
Solution quality estimate total_estimate0.9104
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.8
Skewness Skewness skewness0.043
Kurtosis Kurtosis kurtosis-0.533
Angular range angular_range— – 0.3250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18930000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.990

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6xd9a_
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_idd6xd9b_
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_idd6xd9c_
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_idd6xd9d_
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

8. Citations (1)

9. Files and Curves (10)