7k4m

Crystal structure of MetAP2 Modified Hemoglobin S

Method: X-RAY DIFFRACTION Dmax: 130.9 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 1–142 Chain C; UniProt 1–142 Not recorded Hemoglobin subunit beta × 2 (A0A481SHK9) CMO CARBON MONOXIDE × 4 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH MODE;pH 6.6;293 K;0.2M Na acetate/0.1M Na cacodylate, 30% PEG-8000 Resolution 2.50 Å R-free 0.323
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 1–142 Not recorded Hemoglobin subunit beta × 2 (A0A481SHK9) CMO CARBON MONOXIDE × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH MODE;pH 6.6;293 K;0.2M Na acetate/0.1M Na cacodylate, 30% PEG-8000 Resolution 2.50 Å R-free 0.323
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain G; UniProt 1–142 Chain I; UniProt 1–142 Not recorded Hemoglobin subunit beta × 2 (A0A481SHK9) CMO CARBON MONOXIDE × 4 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH MODE;pH 6.6;293 K;0.2M Na acetate/0.1M Na cacodylate, 30% PEG-8000 Resolution 2.50 Å R-free 0.323

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

Hemoglobin subunit beta

OrganismNot specified

UniProt A0A481SHK9

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 Non-standard monomer:Yes (specific site not provided by mmCIF) Hemoglobin subunit alpha × 2 (P69905) CMO CARBON MONOXIDE × 4 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH MODE;pH 6.6;293 K;0.2M Na acetate/0.1M Na cacodylate, 30% PEG-8000 Resolution 2.50 Å R-free 0.323
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain F; UniProt 1–147 Non-standard monomer:Yes (specific site not provided by mmCIF) Hemoglobin subunit alpha × 2 (P69905) CMO CARBON MONOXIDE × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH MODE;pH 6.6;293 K;0.2M Na acetate/0.1M Na cacodylate, 30% PEG-8000 Resolution 2.50 Å R-free 0.323
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain H; UniProt 1–147 Chain J; UniProt 1–147 Non-standard monomer:Yes (specific site not provided by mmCIF) Hemoglobin subunit alpha × 2 (P69905) CMO CARBON MONOXIDE × 4 HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH MODE;pH 6.6;293 K;0.2M Na acetate/0.1M Na cacodylate, 30% PEG-8000 Resolution 2.50 Å R-free 0.323

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A481SHK9_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 2–148; UniProt 1–147 Author chain D; PDBConstruct 2–148; UniProt 1–147 Author chain F; PDBConstruct 2–148; UniProt 1–147 Author chain H; PDBConstruct 2–148; UniProt 1–147 Author chain J; PDBConstruct 2–148; 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 7k4m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7k4m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7k4m
Deposition date deposition_date2020-09-15
Structure title titleCrystal structure of MetAP2 Modified Hemoglobin S
Keywords keywordsHEMOGLOBIN S, INHIBITOR, ANTISICKLING, 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_guinier39.98
Radius of gyration Rg (electron density) rg_electron39.70
Forward intensity I(0) i0354150000.00
Molecular weight molecular_weight159990.0 kDa
Excluded volume excluded_volume202610 ų
Envelope volume envelope_volume258480 ų
Hydration-shell volume shell_volume55208 ų
Envelope diameter envelope_diameter134.9
Shell Rg shell_rg44.35
Envelope Rg envelope_rg39.05
Shape Rg shape_rg39.70
Total Rg total_rg39.96
Total atoms total_atoms11301
Residues n_residues1428
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 dmax130.9
Rg (real space) rg_real40.02
Rg uncertainty (real space) rg_real_error0.92
I(0) (real space) i0_real3.5410e+08
I(0) uncertainty (real space) i0_real_error6.4870e+06
Rg (reciprocal space) rg_reciprocal40.00
I(0) (reciprocal space) i0_reciprocal354100000.0000
Solution quality estimate total_estimate0.8740
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.3
Skewness Skewness skewness0.313
Kurtosis Kurtosis kurtosis-0.507
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha76840000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.669

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)