8fdk

Phenylhydroxylamine in Reaction with Human Hemoglobin

Method: X-RAY DIFFRACTION Dmax: 69.5 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 Fragment:Shr_HID2 Hemoglobin subunit beta × 2 (P68871) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 NBE NITROSOBENZENE × 5 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH MODE;pH 6.81;298 K;3.2 M sodium/potassium phosphate Resolution 1.89 Å R-free 0.246

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 Non-standard monomer:Yes (specific site not provided by mmCIF) Hemoglobin subunit alpha × 2 (P69905) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 NBE NITROSOBENZENE × 5 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH MODE;pH 6.81;298 K;3.2 M sodium/potassium phosphate Resolution 1.89 Å R-free 0.246

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 8fdk

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8fdk
Deposition date deposition_date2022-12-03
Structure title titlePhenylhydroxylamine in Reaction with Human Hemoglobin
Keywords keywordshemoglobin, phenylhydroxylamine, nitrosobenzene, hemichrome, 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_guinier24.64
Radius of gyration Rg (electron density) rg_electron23.37
Forward intensity I(0) i062604400.00
Molecular weight molecular_weight64222.0 kDa
Excluded volume excluded_volume81257 ų
Envelope volume envelope_volume95907 ų
Hydration-shell volume shell_volume32825 ų
Envelope diameter envelope_diameter71.3
Shell Rg shell_rg31.32
Envelope Rg envelope_rg23.15
Shape Rg shape_rg23.35
Total Rg total_rg24.28
Total atoms total_atoms4540
Residues n_residues566
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 dmax69.5
Rg (real space) rg_real24.40
Rg uncertainty (real space) rg_real_error0.35
I(0) (real space) i0_real6.2600e+07
I(0) uncertainty (real space) i0_real_error8.0010e+05
Rg (reciprocal space) rg_reciprocal24.46
I(0) (reciprocal space) i0_reciprocal62610000.0000
Solution quality estimate total_estimate0.9140
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.0
Skewness Skewness skewness0.011
Kurtosis Kurtosis kurtosis-0.576
Angular range angular_range— – 0.3200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18850000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.990

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id8fdkA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id8fdkC01
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)