6tb2

Structure of human haptoglobin-hemoglobin bound to S. aureus IsdH

Method: X-RAY DIFFRACTION Dmax: 122.8 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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 2–142 Not recorded Hemoglobin subunit beta × 1 (P68871) Haptoglobin × 1 (P00738) Cell wall surface anchor family protein × 2 (A0A0E8IWL6) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277 K;0.2 M sodium citrate tribasic dihydrate, 20 % w/v PEG 3350 Resolution 2.90 Å R-free 0.270

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

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 2–147 Not recorded Hemoglobin subunit alpha × 1 (P69905) Haptoglobin × 1 (P00738) Cell wall surface anchor family protein × 2 (A0A0E8IWL6) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277 K;0.2 M sodium citrate tribasic dihydrate, 20 % w/v PEG 3350 Resolution 2.90 Å R-free 0.270

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 1–146; UniProt 2–147

Haptoglobin

Homo sapiens

UniProt P00738

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain C; UniProt 148–406 Not recorded Hemoglobin subunit alpha × 1 (P69905) Hemoglobin subunit beta × 1 (P68871) Cell wall surface anchor family protein × 2 (A0A0E8IWL6) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277 K;0.2 M sodium citrate tribasic dihydrate, 20 % w/v PEG 3350 Resolution 2.90 Å R-free 0.270

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.

14 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HPT_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 9–267; UniProt 148–406

Cell wall surface anchor family protein

Staphylococcus aureus

UniProt A0A0E8IWL6

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 321–655 Chain E; UniProt 321–655 Not recorded Hemoglobin subunit alpha × 1 (P69905) Hemoglobin subunit beta × 1 (P68871) Haptoglobin × 1 (P00738) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;277 K;0.2 M sodium citrate tribasic dihydrate, 20 % w/v PEG 3350 Resolution 2.90 Å R-free 0.270

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 A0A0E8IWL6_STAAU
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 20–354; UniProt 321–655 Author chain E; PDBConstruct 20–354; UniProt 321–655

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 6tb2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6tb2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6tb2
Deposition date deposition_date2019-10-31
Structure title titleStructure of human haptoglobin-hemoglobin bound to S. aureus IsdH
Keywords keywordsHemoglobin receptor, heme acquisition, inhibitor, METAL TRANSPORT; METAL TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier37.45
Radius of gyration Rg (electron density) rg_electron36.89
Forward intensity I(0) i0274404000.00
Molecular weight molecular_weight137380.0 kDa
Excluded volume excluded_volume173070 ų
Envelope volume envelope_volume230820 ų
Hydration-shell volume shell_volume52200 ų
Envelope diameter envelope_diameter131.0
Shell Rg shell_rg42.96
Envelope Rg envelope_rg36.91
Shape Rg shape_rg36.88
Total Rg total_rg37.32
Total atoms total_atoms9707
Residues n_residues1209
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 dmax122.8
Rg (real space) rg_real37.35
Rg uncertainty (real space) rg_real_error1.01
I(0) (real space) i0_real2.7440e+08
I(0) uncertainty (real space) i0_real_error4.2310e+06
Rg (reciprocal space) rg_reciprocal37.41
I(0) (reciprocal space) i0_reciprocal274400000.0000
Solution quality estimate total_estimate0.8935
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary49.7
Skewness Skewness skewness0.236
Kurtosis Kurtosis kurtosis-0.403
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha52910000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.933

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6tb2a_
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_idd6tb2b_
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 (2 domains)

Domain ID domain_id6tb2A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id6tb2B00
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)