6kye

The crystal structure of recombinant human adult hemoglobin

Method: X-RAY DIFFRACTION Dmax: 137.6 Å Quality: GOOD

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

Hemoglobin subunit alpha

Homo sapiens

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 1–142 Chain C; UniProt 1–142 Not recorded Hemoglobin subunit beta × 2 (P68871) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 CMO CARBON MONOXIDE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:LIQUID DIFFUSION;pH 6;293 K;NaCl, PEG3350, MES Resolution 2.28 Å R-free 0.268
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 1–142 Chain G; UniProt 1–142 Not recorded Hemoglobin subunit beta × 2 (P68871) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 CMO CARBON MONOXIDE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:LIQUID DIFFUSION;pH 6;293 K;NaCl, PEG3350, MES Resolution 2.28 Å R-free 0.268
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain I; UniProt 1–142 Chain K; UniProt 1–142 Not recorded Hemoglobin subunit beta × 2 (P68871) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 CMO CARBON MONOXIDE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:LIQUID DIFFUSION;pH 6;293 K;NaCl, PEG3350, MES Resolution 2.28 Å R-free 0.268

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 410 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 Author chain E; PDBConstruct 1–142; UniProt 1–142 Author chain G; PDBConstruct 1–142; UniProt 1–142 Author chain I; PDBConstruct 1–142; UniProt 1–142 Author chain K; PDBConstruct 1–142; UniProt 1–142

Hemoglobin subunit beta

Homo sapiens

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 1–147 Chain D; UniProt 1–147 Not recorded Hemoglobin subunit alpha × 2 (P69905) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 CMO CARBON MONOXIDE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:LIQUID DIFFUSION;pH 6;293 K;NaCl, PEG3350, MES Resolution 2.28 Å R-free 0.268
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain F; UniProt 1–147 Chain H; UniProt 1–147 Not recorded Hemoglobin subunit alpha × 2 (P69905) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 CMO CARBON MONOXIDE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:LIQUID DIFFUSION;pH 6;293 K;NaCl, PEG3350, MES Resolution 2.28 Å R-free 0.268
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain J; UniProt 1–147 Chain L; UniProt 1–147 Not recorded Hemoglobin subunit alpha × 2 (P69905) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 CMO CARBON MONOXIDE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:LIQUID DIFFUSION;pH 6;293 K;NaCl, PEG3350, MES Resolution 2.28 Å R-free 0.268

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 397 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 Author chain F; PDBConstruct 1–147; UniProt 1–147 Author chain H; PDBConstruct 1–147; UniProt 1–147 Author chain J; PDBConstruct 1–147; UniProt 1–147 Author chain L; 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 6kye

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6kye
Deposition date deposition_date2019-09-18
Structure title titleThe crystal structure of recombinant human adult hemoglobin
Keywords keywordsoxygen transport; OXYGEN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier44.04
Radius of gyration Rg (electron density) rg_electron43.69
Forward intensity I(0) i0505412000.00
Molecular weight molecular_weight192730.0 kDa
Excluded volume excluded_volume243850 ų
Envelope volume envelope_volume321050 ų
Hydration-shell volume shell_volume61177 ų
Envelope diameter envelope_diameter138.1
Shell Rg shell_rg48.59
Envelope Rg envelope_rg42.82
Shape Rg shape_rg43.67
Total Rg total_rg43.96
Total atoms total_atoms13625
Residues n_residues1716
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 dmax137.6
Rg (real space) rg_real44.01
Rg uncertainty (real space) rg_real_error1.31
I(0) (real space) i0_real5.0540e+08
I(0) uncertainty (real space) i0_real_error9.4130e+06
Rg (reciprocal space) rg_reciprocal44.04
I(0) (reciprocal space) i0_reciprocal505400000.0000
Solution quality estimate total_estimate0.8622
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary38.2
Skewness Skewness skewness0.201
Kurtosis Kurtosis kurtosis-0.733
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha286500000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.422

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd6kyea_
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_idd6kyeb_
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_idd6kyec_
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_idd6kyed_
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_idd6kyee_
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_idd6kyef_
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_idd6kyeg_
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_idd6kyeh_
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_idd6kyei_
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_idd6kyej_
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_idd6kyek_
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_idd6kyel_
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 (12 domains)

Domain ID domain_id6kyeA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6kyeB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6kyeC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6kyeD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6kyeE00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6kyeF00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6kyeG00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6kyeH00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6kyeI00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6kyeJ00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6kyeK00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6kyeL00
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)