8vyl

The structure of Human Hemoglobin in Complex with Nanobody BtNbE11

Method: X-RAY DIFFRACTION Dmax: 125.4 Å Quality: REASONABLE

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–142 Chain C; UniProt 1–142 Not recorded Hemoglobin subunit beta × 2 (P68871) Nanobody BtNbE11 × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 ACE ACETYL GROUP × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;293 K;0.1-0.3M NH4 Acet. pH 5.5, 0.1-0.3M Na Acet., 25% w/v PEG3350 Resolution 2.02 Å R-free 0.266

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 1–142; UniProt 1–142 Author chain C; PDBConstruct 1–142; UniProt 1–142

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 1–147 Chain D; UniProt 1–147 Not recorded Hemoglobin subunit alpha × 2 (P69905) Nanobody BtNbE11 × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 ACE ACETYL GROUP × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;293 K;0.1-0.3M NH4 Acet. pH 5.5, 0.1-0.3M Na Acet., 25% w/v PEG3350 Resolution 2.02 Å R-free 0.266

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 1–147; UniProt 1–147 Author chain D; PDBConstruct 1–147; UniProt 1–147

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 8vyl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8vyl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8vyl
Deposition date deposition_date2024-02-08
Structure title titleThe structure of Human Hemoglobin in Complex with Nanobody BtNbE11
Keywords keywordsHemoglobin, Nanobody, 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_guinier32.73
Radius of gyration Rg (electron density) rg_electron32.37
Forward intensity I(0) i0124209000.00
Molecular weight molecular_weight90593.0 kDa
Excluded volume excluded_volume113840 ų
Envelope volume envelope_volume139330 ų
Hydration-shell volume shell_volume38698 ų
Envelope diameter envelope_diameter137.4
Shell Rg shell_rg36.06
Envelope Rg envelope_rg32.77
Shape Rg shape_rg32.35
Total Rg total_rg32.72
Total atoms total_atoms6433
Residues n_residues820
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 dmax125.4
Rg (real space) rg_real33.22
Rg uncertainty (real space) rg_real_error1.29
I(0) (real space) i0_real1.2420e+08
I(0) uncertainty (real space) i0_real_error2.0440e+06
Rg (reciprocal space) rg_reciprocal33.01
I(0) (reciprocal space) i0_reciprocal124200000.0000
Solution quality estimate total_estimate0.7448
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.0
Skewness Skewness skewness0.780
Kurtosis Kurtosis kurtosis0.504
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha24110000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.460; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.654; Smooth: 0.643

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)