5x2u

Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin after Adding 80 mM phosphate pH 6.7.

Method: X-RAY DIFFRACTION Dmax: 142.8 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 Chain C; UniProt 2–142 Not recorded Hemoglobin subunit beta × 2 (P68871) HNI PROTOPORPHYRIN IX CONTAINING NI(II) × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 7.7;293 K;17%(w/v) PEG 3350, pH 7.7 Resolution 2.53 Å R-free 0.274
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 2–142 Chain G; UniProt 2–142 Not recorded Hemoglobin subunit beta × 2 (P68871) HNI PROTOPORPHYRIN IX CONTAINING NI(II) × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 7.7;293 K;17%(w/v) PEG 3350, pH 7.7 Resolution 2.53 Å R-free 0.274
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain I; UniProt 2–142 Chain K; UniProt 2–142 Not recorded Hemoglobin subunit beta × 2 (P68871) HNI PROTOPORPHYRIN IX CONTAINING NI(II) × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 7.7;293 K;17%(w/v) PEG 3350, pH 7.7 Resolution 2.53 Å R-free 0.274

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 1–141; UniProt 2–142 Author chain C; PDBConstruct 1–141; UniProt 2–142 Author chain E; PDBConstruct 1–141; UniProt 2–142 Author chain G; PDBConstruct 1–141; UniProt 2–142 Author chain I; PDBConstruct 1–141; UniProt 2–142 Author chain K; 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) HNI PROTOPORPHYRIN IX CONTAINING NI(II) × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 7.7;293 K;17%(w/v) PEG 3350, pH 7.7 Resolution 2.53 Å R-free 0.274
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain F; UniProt 2–147 Chain H; UniProt 2–147 Not recorded Hemoglobin subunit alpha × 2 (P69905) HNI PROTOPORPHYRIN IX CONTAINING NI(II) × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 7.7;293 K;17%(w/v) PEG 3350, pH 7.7 Resolution 2.53 Å R-free 0.274
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain J; UniProt 2–147 Chain L; UniProt 2–147 Not recorded Hemoglobin subunit alpha × 2 (P69905) HNI PROTOPORPHYRIN IX CONTAINING NI(II) × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 7.7;293 K;17%(w/v) PEG 3350, pH 7.7 Resolution 2.53 Å R-free 0.274

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 1–146; UniProt 2–147 Author chain D; PDBConstruct 1–146; UniProt 2–147 Author chain F; PDBConstruct 1–146; UniProt 2–147 Author chain H; PDBConstruct 1–146; UniProt 2–147 Author chain J; PDBConstruct 1–146; UniProt 2–147 Author chain L; 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 5x2u

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5x2u
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5x2u
Deposition date deposition_date2017-02-02
Structure title titleDirect Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin after Adding 80 mM phosphate pH 6.7.
Keywords keywordsHemoglobin, Allostery, Allosteric proteins, Oxygen binding, Bezafibrate, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier43.80
Radius of gyration Rg (electron density) rg_electron43.44
Forward intensity I(0) i0503825000.00
Molecular weight molecular_weight191710.0 kDa
Excluded volume excluded_volume242380 ų
Envelope volume envelope_volume322210 ų
Hydration-shell volume shell_volume61763 ų
Envelope diameter envelope_diameter141.8
Shell Rg shell_rg48.38
Envelope Rg envelope_rg42.53
Shape Rg shape_rg43.42
Total Rg total_rg43.73
Total atoms total_atoms13548
Residues n_residues1710
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 dmax142.8
Rg (real space) rg_real43.79
Rg uncertainty (real space) rg_real_error1.41
I(0) (real space) i0_real5.0380e+08
I(0) uncertainty (real space) i0_real_error9.5540e+06
Rg (reciprocal space) rg_reciprocal43.80
I(0) (reciprocal space) i0_reciprocal503800000.0000
Solution quality estimate total_estimate0.8780
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.6
Skewness Skewness skewness0.232
Kurtosis Kurtosis kurtosis-0.665
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha205400000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.762

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd5x2ua_
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_idd5x2ub_
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_idd5x2uc_
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_idd5x2ud_
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_idd5x2ue_
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_idd5x2uf_
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_idd5x2ug_
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_idd5x2uh_
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_idd5x2ui_
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_idd5x2uj_
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_idd5x2uk_
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_idd5x2ul_
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_id5x2uA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5x2uB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5x2uC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5x2uD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5x2uE00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5x2uF00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5x2uG00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5x2uH00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5x2uI00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5x2uJ00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5x2uK00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5x2uL00
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)