SAXSdb — 6otx

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

Hemoglobin II

Phacoides pectinatus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Hemoglobin III × 1 （P41262） PROTOPORPHYRIN IX CONTAINING FE × 2 OXYGEN MOLECULE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q86G74_PHAPT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–152； UniProt 1–152

Hemoglobin III

Phacoides pectinatus

UniProt P41262

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Hemoglobin II × 1 （Q86G74） PROTOPORPHYRIN IX CONTAINING FE × 2 OXYGEN MOLECULE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLB3_PHAPT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–152； UniProt 2–153

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	6otx
Deposition date deposition_date	2019-05-03
Structure title title	Crystallographic Structure of (HbII-HbIII)-O2 from Lucina pectinata at pH 7.0
Keywords keywords	hemeprotein, OXYGEN TRANSPORT; OXYGEN TRANSPORT
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.

6otx__assembly_1__model_1

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

Download this curve (.dat)

6otx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6otx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.51 Å
Rg (electron density)	19.28 Å
Total Rg	20.15 Å
Atom count	2503
Residues	303
Excluded volume	44604 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6otx__assembly_1__model_1`	dimeric （2）	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 (5)

Entity 1 Entity 1 polymer

Description description	Hemoglobin II
Molecular weight formula_weight	17146.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2548

MTTLTNPQKAAIRSSWSKFMDNGVSNGQGFYMDLFKAHPETLTPFKSLFGGLTLAQLQDNPKMKAQSLVFCNGMSSFVDHLDDNDMLVVLIQKMAKLHNNRGIRASDLRTAYDILIHYMEDHNHMVGGAKDAWEVFVGFICKTLGDYMKELS

Source Source

Source organism organism	Phacoides pectinatus
Common name common_name	Thick lucine
NCBI taxonomy ID ncbi_taxonomy_id	244486
Host organism host_organism	Phacoides pectinatus

Entity 2 Entity 2 polymer

Description description	Hemoglobin III
Molecular weight formula_weight	17450.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SSGLTGPQKAALKSSWSRFMDNAVTNGTNFYMDLFKAYPDTLTPFKSLFEDVSFNQMTDHPTMKAQALVFCDGMSSFVDNLDDHEVLVVLLQKMAKLHFNRGIRIKELRDGYGVLLRYLEDHCHVEGSTKNAWEDFIAYICRVQGDFMKERL

Source Source

Source organism organism	Phacoides pectinatus
Common name common_name	Thick lucine
NCBI taxonomy ID ncbi_taxonomy_id	244486
Host organism host_organism	Phacoides pectinatus

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	2

Entity 4 Entity 4 non-polymer

Description description	OXYGEN MOLECULE
Molecular weight formula_weight	32.0 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	39

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6otxa_
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.1.1.0 — automated matches

Domain ID domain_id	d6otxb_
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.1.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	6otxA00
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	6otxB00
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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Unit-cell length a length_a	74.736 Å
Unit-cell length b length_b	74.736 Å
Unit-cell length c length_c	152.571 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	2.539 Å
Low-resolution limit resolution_low	33.558 Å
R factor r_factor	0.1952
R_work r_work	0.1922
R_free r_free	0.2488

Crystallographic Structure of (HbII-HbIII)-O2 from Lucina pectinata at pH 7.0

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

Hemoglobin II

State in the Current Structure

Other States of the Same Protein in the Database

Hemoglobin III

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

6otx__assembly_1__model_1

6otx__assembly_1__model_1 | I(q)

6otx__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystallographic Structure of (HbII-HbIII)-O2 from Lucina pectinata at pH 7.0

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

Hemoglobin II

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 III

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

6otx__assembly_1__model_1

6otx__assembly_1__model_1 | I(q)

6otx__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)