3d7o

Human hemoglobin, nitrogen dioxide anion modified

Method: X-RAY DIFFRACTION Dmax: 59.7 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 Not recorded Hemoglobin subunit beta × 2 (P68871) NO2 NITRITE ION × 4 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 MBN TOLUENE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:LIQUID DIFFUSION;pH 6.8;295 K;Sodium phosphate, Potassium phosphate, Toluene, Hemoglobin, pH 6.8, LIQUID DIFFUSION, temperature 295K Resolution 1.80 Å R-free 0.237

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

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 Not recorded Hemoglobin subunit alpha × 2 (P69905) NO2 NITRITE ION × 4 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 MBN TOLUENE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:LIQUID DIFFUSION;pH 6.8;295 K;Sodium phosphate, Potassium phosphate, Toluene, Hemoglobin, pH 6.8, LIQUID DIFFUSION, temperature 295K Resolution 1.80 Å R-free 0.237

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

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 3d7o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3d7o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3d7o
Deposition date deposition_date2008-05-21
Structure title titleHuman hemoglobin, nitrogen dioxide anion modified
Keywords keywords;Human Hemoglobin, Acetylation, Disease mutation, Glycation, Glycoprotein, Heme, Iron, Metal-binding, Oxygen transport, Polymorphism, Transport, Hypotensive agent, Pyruvate, S-nitrosylation, Vasoactive ;; OXYGEN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.25
Radius of gyration Rg (electron density) rg_electron19.01
Forward intensity I(0) i017177700.00
Molecular weight molecular_weight32412.0 kDa
Excluded volume excluded_volume40978 ų
Envelope volume envelope_volume46645 ų
Hydration-shell volume shell_volume20258 ų
Envelope diameter envelope_diameter59.6
Shell Rg shell_rg25.43
Envelope Rg envelope_rg19.16
Shape Rg shape_rg19.01
Total Rg total_rg19.96
Total atoms total_atoms2291
Residues n_residues287
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 dmax59.7
Rg (real space) rg_real20.13
Rg uncertainty (real space) rg_real_error0.23
I(0) (real space) i0_real1.7180e+07
I(0) uncertainty (real space) i0_real_error2.0770e+05
Rg (reciprocal space) rg_reciprocal20.16
I(0) (reciprocal space) i0_reciprocal17180000.0000
Solution quality estimate total_estimate0.7775
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary58.8
Skewness Skewness skewness0.110
Kurtosis Kurtosis kurtosis-0.569
Angular range angular_range— – 0.3950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3365000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.969; Stabil: 1.000; Sysdev: 0.406; Positv: 1.000; Valcen: 0.992; Smooth: 0.987

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3d7oa_
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_idd3d7ob_
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 (2 domains)

Domain ID domain_id3d7oA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id3d7oB00
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)