9hba

Crystal structure of C35 bound to Hem

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Hemoglobin subunit alpha

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Hemoglobin subunit beta × 2 （P68871） PROTOPORPHYRIN IX CONTAINING FE × 4 GLYCEROL × 6 4-[2-[[5-(1H-indol-3-yl)-1,3,4-oxadiazol-2-yl]sulfanyl]ethanoylamino]benzoic acid × 3 DIMETHYL SULFOXIDE × 8 CARBON MONOXIDE × 4 ACETIC ACID × 2 SULFATE ION × 16 TRIETHYLENE GLYCOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

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

Homo sapiens

UniProt P68871

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Hemoglobin subunit alpha × 2 （P69905） PROTOPORPHYRIN IX CONTAINING FE × 4 GLYCEROL × 6 4-[2-[[5-(1H-indol-3-yl)-1,3,4-oxadiazol-2-yl]sulfanyl]ethanoylamino]benzoic acid × 3 DIMETHYL SULFOXIDE × 8 CARBON MONOXIDE × 4 ACETIC ACID × 2 SULFATE ION × 16 TRIETHYLENE GLYCOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

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

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9hba
Deposition date deposition_date	2024-11-05
Last revision last_revision	2025-11-19
Structure title title	Crystal structure of C35 bound to Hem
Keywords keywords	Inhibitor, drug discovery, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9hba__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9hba__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9hba__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	24.64 Å
Rg (electron density)	23.38 Å
Total Rg	24.32 Å
Atom count	4775
Residues	572
Excluded volume	84875 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9hba__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	Hemoglobin subunit alpha
Molecular weight formula_weight	15150.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	5136

VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Hemoglobin subunit beta
Molecular weight formula_weight	15890.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	4-[2-[[5-(1H-indol-3-yl)-1,3,4-oxadiazol-2-yl]sulfanyl]ethanoylamino]benzoic acid
Molecular weight formula_weight	394.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 7 Entity 7 non-polymer

Description description	CARBON MONOXIDE
Molecular weight formula_weight	28.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 10 Entity 10 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	323

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Unit-cell length a length_a	92.178 Å
Unit-cell length b length_b	92.178 Å
Unit-cell length c length_c	142.973 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.510 Å
Low-resolution limit resolution_low	53.255 Å
R factor r_factor	—
R_work r_work	0.1844
R_free r_free	0.2149

Crystal structure of C35 bound to Hem

1. Protein Identity and Related Structures Protein Identity & Related Structures

Hemoglobin subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Hemoglobin subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9hba__assembly_1__model_1

9hba__assembly_1__model_1 | I(q)

9hba__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

7. Citations (1)

Crystal structure of C35 bound to Hem

1. Protein Identity and Related Structures Protein Identity & Related Structures

Hemoglobin subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Hemoglobin subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9hba__assembly_1__model_1

9hba__assembly_1__model_1 | I(q)

9hba__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

7. Citations (1)