6kai

Crosslinked alpha(Ni)-beta(Fe) human hemoglobin A in the T quaternary structure at 95 K: Light

Method: X-RAY DIFFRACTION Dmax: 124.0 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 CMO CARBON MONOXIDE × 7 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 2FU BUT-2-ENEDIAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 6.6;293 K;20%w/v PEG 3350, 50 mM citrate-ammonium buffer, 150 mM dipotassium sulfate Resolution 1.45 Å R-free 0.202
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 CMO CARBON MONOXIDE × 8 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 2FU BUT-2-ENEDIAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 6.6;293 K;20%w/v PEG 3350, 50 mM citrate-ammonium buffer, 150 mM dipotassium sulfate Resolution 1.45 Å R-free 0.202

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 411 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

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 CMO CARBON MONOXIDE × 7 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 2FU BUT-2-ENEDIAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 6.6;293 K;20%w/v PEG 3350, 50 mM citrate-ammonium buffer, 150 mM dipotassium sulfate Resolution 1.45 Å R-free 0.202
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 CMO CARBON MONOXIDE × 8 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 2FU BUT-2-ENEDIAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 6.6;293 K;20%w/v PEG 3350, 50 mM citrate-ammonium buffer, 150 mM dipotassium sulfate Resolution 1.45 Å R-free 0.202

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 398 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

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 6kai

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6kai
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id6kai
Deposition date deposition_date2019-06-23
Structure title titleCrosslinked alpha(Ni)-beta(Fe) human hemoglobin A in the T quaternary structure at 95 K: Light
Keywords keywordsHemoglobin, Photolysis, Hybrid, 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_guinier38.44
Radius of gyration Rg (electron density) rg_electron38.25
Forward intensity I(0) i0235929000.00
Molecular weight molecular_weight129510.0 kDa
Excluded volume excluded_volume163700 ų
Envelope volume envelope_volume208860 ų
Hydration-shell volume shell_volume46002 ų
Envelope diameter envelope_diameter124.5
Shell Rg shell_rg43.69
Envelope Rg envelope_rg37.63
Shape Rg shape_rg38.25
Total Rg total_rg38.57
Total atoms total_atoms9154
Residues n_residues1148
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 dmax124.0
Rg (real space) rg_real38.64
Rg uncertainty (real space) rg_real_error1.24
I(0) (real space) i0_real2.3590e+08
I(0) uncertainty (real space) i0_real_error4.1630e+06
Rg (reciprocal space) rg_reciprocal38.52
I(0) (reciprocal space) i0_reciprocal235900000.0000
Solution quality estimate total_estimate0.7896
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary36.3
Skewness Skewness skewness0.370
Kurtosis Kurtosis kurtosis-0.722
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha74510000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.775; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd6kaia_
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_idd6kaib_
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_idd6kaic_
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_idd6kaid_
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_idd6kaie_
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_idd6kaif_
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_idd6kaig_
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_idd6kaih_
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 (8 domains)

Domain ID domain_id6kaiA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6kaiB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6kaiC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6kaiD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6kaiE00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6kaiF00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6kaiG00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6kaiH00
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)