SAXSdb — 1hdb

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

HEMOGLOBIN (DEOXY) BETA-V67T

Homo sapiens

UniProt P01922

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 1–141 Chain C； UniProt 1–141	Mutation：CHAIN B, D, V67T	HEMOGLOBIN (DEOXY) BETA-V67T × 2 （P02023） HEM PROTOPORPHYRIN IX CONTAINING FE × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.20 Å

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.

Other PDB	Difference from Current Entry 1HDB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NQP Crystal structure of Human hemoglobin E at 1.73 A resolution Deposited 2003-01-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain not uniquely mapped Reference range not declared Chain C 1–141（141 aa）	Not recorded	CYN CYANIDE ION × 4 HEM PROTOPORPHYRIN IX CONTAINING FE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG and Glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.73 Å R-free 0.211
1XYE T-to-THigh Transitions in Human Hemoglobin: alpha Y42A deoxy low salt Deposited 2004-11-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–141（141 aa） Chain C 1–141（141 aa）	Mutation：V1M, Y42A Mutation：V1M, Y42A	HEM PROTOPORPHYRIN IX CONTAINING FE × 4	X-RAY DIFFRACTION X-ray crystallization conditions batch；pH 7；298 K；10% PEG 6000, 10 mM potassium phosphate, 100 mM potassium chloride, 3 mM sodium dithionite, 10 mg/ml Hb, pH 7.0, batch, temperature 298K	Resolution 2.13 Å R-free 0.241
1XZ2 wild-type hemoglobin deoxy no-salt Deposited 2004-11-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–141（141 aa） Chain C 1–141（141 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4	X-RAY DIFFRACTION X-ray crystallization conditions batch；pH 7；298 K；12% PEG 1450, 10 mg/ml Hb, pH 7.0, batch, temperature 298.0K	Resolution 1.90 Å R-free 0.201
1XZ4 Intersubunit Interactions Associated with Tyr42alpha Stabilize the Quaternary-T Tetramer but are not Major Quaternary Constraints in Deoxyhemoglobin: alphaY42A deoxyhemoglobin no-salt Deposited 2004-11-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–141（141 aa） Chain C 1–141（141 aa）	Mutation：V1M, Y42A Mutation：V1M, Y42A	HEM PROTOPORPHYRIN IX CONTAINING FE × 4	X-RAY DIFFRACTION X-ray crystallization conditions batch；pH 4.6；298 K；15% PEG 4000, 50 mM sodium acetate, 100 mM ammonium acetate, 3 mM sodium dithionite, 20 mg/ml Hb, pH 4.6, batch, temperature 298K	Resolution 2.00 Å R-free 0.224
2HHB THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT 1.74 ANGSTROMS RESOLUTION Deposited 1984-03-07	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–141（141 aa） Chain C 1–141（141 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.74 Å
2HHD OXYGEN AFFINITY MODULATION BY THE N-TERMINI OF THE BETA-CHAINS IN HUMAN AND BOVINE HEMOGLOBIN Deposited 1994-09-29	Different mutation/modification	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–141（141 aa） Chain C 1–141（141 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
3HHB THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT 1.74 ANGSTROMS RESOLUTION Deposited 1984-03-07	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–141（141 aa） Chain C 1–141（141 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.74 Å

7 other PDB entries and 7 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 1–141 Author chain C； PDBConstruct 1–141； UniProt 1–141

HEMOGLOBIN (DEOXY) BETA-V67T

Homo sapiens

UniProt P02023

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 1–146 Chain D； UniProt 1–146	Mutation：CHAIN B, D, V67T	HEMOGLOBIN (DEOXY) BETA-V67T × 2 （P01922） HEM PROTOPORPHYRIN IX CONTAINING FE × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.20 Å

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.

Other PDB	Difference from Current Entry 1HDB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BUW CRYSTAL STRUCTURE OF S-NITROSO-NITROSYL HUMAN HEMOGLOBIN A Deposited 1998-09-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–146（146 aa） Chain D 1–146（146 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 NO NITRIC OXIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；1% PROTEIN 100 MM SODIUM CACODYLATE, PH 5.8 16% PEG 6000	Resolution 1.90 Å R-free 0.244
1NQP Crystal structure of Human hemoglobin E at 1.73 A resolution Deposited 2003-01-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain not uniquely mapped Reference range not declared Chain D 1–146（146 aa）	Not recorded	CYN CYANIDE ION × 4 HEM PROTOPORPHYRIN IX CONTAINING FE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG and Glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.73 Å R-free 0.211
2HHB THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT 1.74 ANGSTROMS RESOLUTION Deposited 1984-03-07	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–146（146 aa） Chain D 1–146（146 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.74 Å
3HHB THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT 1.74 ANGSTROMS RESOLUTION Deposited 1984-03-07	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–146（146 aa） Chain D 1–146（146 aa）	Not recorded	HEM PROTOPORPHYRIN IX CONTAINING FE × 4 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.74 Å

4 other PDB entries and 4 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 1–146 Author chain D； PDBConstruct 1–146； UniProt 1–146

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	1hdb
Deposition date deposition_date	1995-04-14
Structure title title	ANALYSIS OF THE CRYSTAL STRUCTURE, MOLECULAR MODELING AND INFRARED SPECTROSCOPY OF THE DISTAL BETA-HEME POCKET VALINE67(E11)-THREONINE MUTATION OF HEMOGLOBIN
Keywords keywords	HUMAN HEMOGLOBIN, DEOXY-BETA-V67T, OXYGEN TRANSPORT; OXYGEN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	24.92 Å
Radius of gyration Rg (electron density) rg_electron	23.62 Å
Forward intensity I(0) i0	64437500.00
Molecular weight molecular_weight	64651.0 kDa
Excluded volume excluded_volume	81635 Å³
Envelope volume envelope_volume	97066 Å³
Hydration-shell volume shell_volume	32950 Å³
Envelope diameter envelope_diameter	70.8 Å
Shell Rg shell_rg	31.72 Å
Envelope Rg envelope_rg	23.29 Å
Shape Rg shape_rg	23.61 Å
Total Rg total_rg	24.54 Å
Total atoms total_atoms	4566
Residues n_residues	574
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	75.3 Å
Rg (real space) rg_real	24.66 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	6.4440e+07
I(0) uncertainty (real space) i0_real_error	7.8770e+05
Rg (reciprocal space) rg_reciprocal	24.72 Å
I(0) (reciprocal space) i0_reciprocal	64440000.0000
Solution quality estimate total_estimate	0.8235
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.5 Å
Skewness Skewness skewness	-0.001
Kurtosis Kurtosis kurtosis	-0.572
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15690000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	HEMOGLOBIN (DEOXY) BETA-V67T
Molecular weight formula_weight	15150.4 kDa
Mutation mutation	CHAIN B, D, V67T
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	5000

VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	HEMOGLOBIN (DEOXY) BETA-V67T
Molecular weight formula_weight	15892.2 kDa
Mutation mutation	CHAIN B, D, V67T
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKTLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

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	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	434

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1hdba_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.2 — Globins

Domain ID domain_id	d1hdbb_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.2 — Globins

Domain ID domain_id	d1hdbc_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.2 — Globins

Domain ID domain_id	d1hdbd_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.2 — Globins

CATH v4.4 (4 domains)

Domain ID domain_id	1hdbA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1hdbB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1hdbC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

Domain ID domain_id	1hdbD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

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8. Citations (2)

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Unit-cell length a length_a	63.540 Å
Unit-cell length b length_b	83.190 Å
Unit-cell length c length_c	54.020 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.15 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1490
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/hd/1hdb/1hdb.fit
pddf	/app/data/pr_computation/hd/1hdb/1hdb.pr.out
profile	/app/data/saxs_computation/hd/1hdb/1hdb.dat

ANALYSIS OF THE CRYSTAL STRUCTURE, MOLECULAR MODELING AND INFRARED SPECTROSCOPY OF THE DISTAL BETA-HEME POCKET VALINE67(E11)-THREONINE MUTATION OF HEMOGLOBIN

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

HEMOGLOBIN (DEOXY) BETA-V67T

State in the Current Structure

Other States of the Same Protein in the Database

HEMOGLOBIN (DEOXY) BETA-V67T

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)