5e29

Crystal Structure of Deoxygenated Hemoglobin in Complex with an Allosteric Effector and Nitric Oxide

Method: X-RAY DIFFRACTION Dmax: 70.4 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 Not recorded Hemoglobin subunit beta × 2 (P68871) NO NITRIC OXIDE × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 5JN 2-(nitrooxy)ethyl 2-(4-{2-[(3,5-dimethylphenyl)amino]-2-oxoethyl}phenoxy)-2-methylpropanoate × 1 RQ3 2-{4-[(3,5-DIMETHYLANILINO)-CARBONYL-METHYL]-PHENOXY}-2-METHYLPROPIONIC ACID × 2 NO3 NITRATE ION × 2 CAC CACODYLATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIQUID DIFFUSION;pH 6.5;295 K;0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, 30% w/v PEG8000, anaerobic conditions Resolution 1.85 Å R-free 0.253

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 3–147 Chain D; UniProt 3–147 Not recorded Hemoglobin subunit alpha × 2 (P69905) NO NITRIC OXIDE × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 5JN 2-(nitrooxy)ethyl 2-(4-{2-[(3,5-dimethylphenyl)amino]-2-oxoethyl}phenoxy)-2-methylpropanoate × 1 RQ3 2-{4-[(3,5-DIMETHYLANILINO)-CARBONYL-METHYL]-PHENOXY}-2-METHYLPROPIONIC ACID × 2 NO3 NITRATE ION × 2 CAC CACODYLATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIQUID DIFFUSION;pH 6.5;295 K;0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, 30% w/v PEG8000, anaerobic conditions Resolution 1.85 Å R-free 0.253

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 1–145; UniProt 3–147 Author chain D; PDBConstruct 1–145; UniProt 3–147

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 5e29

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5e29
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5e29
Deposition date deposition_date2015-09-30
Structure title titleCrystal Structure of Deoxygenated Hemoglobin in Complex with an Allosteric Effector and Nitric Oxide
Keywords keywordshemoglobin, right-shifter, nitric oxide, 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_guinier24.68
Radius of gyration Rg (electron density) rg_electron23.36
Forward intensity I(0) i065541400.00
Molecular weight molecular_weight65350.0 kDa
Excluded volume excluded_volume82523 ų
Envelope volume envelope_volume96280 ų
Hydration-shell volume shell_volume32886 ų
Envelope diameter envelope_diameter71.7
Shell Rg shell_rg31.50
Envelope Rg envelope_rg23.17
Shape Rg shape_rg23.35
Total Rg total_rg24.28
Total atoms total_atoms4615
Residues n_residues572
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 dmax70.4
Rg (real space) rg_real24.43
Rg uncertainty (real space) rg_real_error0.26
I(0) (real space) i0_real6.5540e+07
I(0) uncertainty (real space) i0_real_error7.3250e+05
Rg (reciprocal space) rg_reciprocal24.49
I(0) (reciprocal space) i0_reciprocal65540000.0000
Solution quality estimate total_estimate0.9127
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.5
Skewness Skewness skewness0.012
Kurtosis Kurtosis kurtosis-0.567
Angular range angular_range— – 0.3200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16620000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.991

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5e29a_
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_idd5e29b_
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_idd5e29c_
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_idd5e29d_
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 (4 domains)

Domain ID domain_id5e29A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5e29B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5e29C00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5e29D00
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)