6lcx

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

Method: X-RAY DIFFRACTION Dmax: 123.9 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) × 4 2FU BUT-2-ENEDIAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 6.6;293 K;1.0% (w/v) protein solution that contains 18% (w/v) PEG 3350, 0.15 M dipotassium sulfate, 50 mM citrate-ammonium buffer (pH 6.6) Resolution 1.40 Å R-free 0.216
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) × 4 2FU BUT-2-ENEDIAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 6.6;293 K;1.0% (w/v) protein solution that contains 18% (w/v) PEG 3350, 0.15 M dipotassium sulfate, 50 mM citrate-ammonium buffer (pH 6.6) Resolution 1.40 Å R-free 0.216

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) × 4 2FU BUT-2-ENEDIAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 6.6;293 K;1.0% (w/v) protein solution that contains 18% (w/v) PEG 3350, 0.15 M dipotassium sulfate, 50 mM citrate-ammonium buffer (pH 6.6) Resolution 1.40 Å R-free 0.216
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) × 4 2FU BUT-2-ENEDIAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:MICROBATCH;pH 6.6;293 K;1.0% (w/v) protein solution that contains 18% (w/v) PEG 3350, 0.15 M dipotassium sulfate, 50 mM citrate-ammonium buffer (pH 6.6) Resolution 1.40 Å R-free 0.216

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 6lcx

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6lcx
Deposition date deposition_date2019-11-20
Structure title titleCrosslinked alpha(Ni)-beta(Ni) human hemoglobin A in the T quaternary structure at 95 K: Light
Keywords keywordsHemoglobin, Photolysis, 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_guinier38.48
Radius of gyration Rg (electron density) rg_electron38.28
Forward intensity I(0) i0233921000.00
Molecular weight molecular_weight129100.0 kDa
Excluded volume excluded_volume163300 ų
Envelope volume envelope_volume208950 ų
Hydration-shell volume shell_volume46057 ų
Envelope diameter envelope_diameter124.5
Shell Rg shell_rg43.68
Envelope Rg envelope_rg37.61
Shape Rg shape_rg38.28
Total Rg total_rg38.60
Total atoms total_atoms9124
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 dmax123.9
Rg (real space) rg_real38.68
Rg uncertainty (real space) rg_real_error1.09
I(0) (real space) i0_real2.3390e+08
I(0) uncertainty (real space) i0_real_error4.0580e+06
Rg (reciprocal space) rg_reciprocal38.56
I(0) (reciprocal space) i0_reciprocal233900000.0000
Solution quality estimate total_estimate0.8444
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary36.3
Skewness Skewness skewness0.371
Kurtosis Kurtosis kurtosis-0.723
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha78980000.0000
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: 0.937; Smooth: 0.712

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd6lcxa_
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_idd6lcxb_
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_idd6lcxc_
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_idd6lcxd_
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_idd6lcxe_
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_idd6lcxf_
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_idd6lcxg_
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_idd6lcxh_
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_id6lcxA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6lcxB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6lcxC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6lcxD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6lcxE00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6lcxF00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6lcxG00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6lcxH00
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)