SAXSdb — 2d2n

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

Giant hemoglobin, A1(b) globin chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	Giant hemoglobin, A2(a5) globin chain × 6 （Q7M413） Giant hemoglobin, B2(c) globin chain × 6 （Q7M418） Giant hemoglobin, B1(d) globin chain × 6 （Q5KSB7） PROTOPORPHYRIN IX CONTAINING FE × 24 OXYGEN MOLECULE × 24 METHYL MERCURY ION × 24	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Giant hemoglobin, A2(a5) globin chain × 1 （Q7M413） Giant hemoglobin, B2(c) globin chain × 1 （Q7M418） Giant hemoglobin, B1(d) globin chain × 1 （Q5KSB7） PROTOPORPHYRIN IX CONTAINING FE × 4 OXYGEN MOLECULE × 4 METHYL MERCURY ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLBB_OLIMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–140； UniProt 17–156

Giant hemoglobin, A2(a5) globin chain

OrganismNot specified

UniProt Q7M413

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	Giant hemoglobin, A1(b) globin chain × 6 （Q7M419） Giant hemoglobin, B2(c) globin chain × 6 （Q7M418） Giant hemoglobin, B1(d) globin chain × 6 （Q5KSB7） PROTOPORPHYRIN IX CONTAINING FE × 24 OXYGEN MOLECULE × 24 METHYL MERCURY ION × 24	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Giant hemoglobin, A1(b) globin chain × 1 （Q7M419） Giant hemoglobin, B2(c) globin chain × 1 （Q7M418） Giant hemoglobin, B1(d) globin chain × 1 （Q5KSB7） PROTOPORPHYRIN IX CONTAINING FE × 4 OXYGEN MOLECULE × 4 METHYL MERCURY ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLB5_OLIMA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–142； UniProt 17–158

Giant hemoglobin, B2(c) globin chain

OrganismNot specified

UniProt Q7M418

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	Giant hemoglobin, A1(b) globin chain × 6 （Q7M419） Giant hemoglobin, A2(a5) globin chain × 6 （Q7M413） Giant hemoglobin, B1(d) globin chain × 6 （Q5KSB7） PROTOPORPHYRIN IX CONTAINING FE × 24 OXYGEN MOLECULE × 24 METHYL MERCURY ION × 24	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Giant hemoglobin, A1(b) globin chain × 1 （Q7M419） Giant hemoglobin, A2(a5) globin chain × 1 （Q7M413） Giant hemoglobin, B1(d) globin chain × 1 （Q5KSB7） PROTOPORPHYRIN IX CONTAINING FE × 4 OXYGEN MOLECULE × 4 METHYL MERCURY ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLBC_OLIMA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–147； UniProt 17–163

Giant hemoglobin, B1(d) globin chain

OrganismNot specified

UniProt Q5KSB7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	Giant hemoglobin, A1(b) globin chain × 6 （Q7M419） Giant hemoglobin, A2(a5) globin chain × 6 （Q7M413） Giant hemoglobin, B2(c) globin chain × 6 （Q7M418） PROTOPORPHYRIN IX CONTAINING FE × 24 OXYGEN MOLECULE × 24 METHYL MERCURY ION × 24	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Giant hemoglobin, A1(b) globin chain × 1 （Q7M419） Giant hemoglobin, A2(a5) globin chain × 1 （Q7M413） Giant hemoglobin, B2(c) globin chain × 1 （Q7M418） PROTOPORPHYRIN IX CONTAINING FE × 4 OXYGEN MOLECULE × 4 METHYL MERCURY ION × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5KSB7_OLIMA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–145； UniProt 17–161

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	2d2n
Deposition date deposition_date	2005-09-12
Structure title title	Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi
Keywords keywords	GIANT HEMOGLOBIN, SULFIDE BINDING, INVERTEBRATE, POGONOPHORA, OLIGOBRACHIA MASHIKOI, OXYGEN STORAGE-TRANSPORT COMPLEX; OXYGEN STORAGE/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.

2d2n__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2d2n__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2d2n__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	26.27 Å
Rg (electron density)	25.27 Å
Total Rg	25.97 Å
Atom count	4452
Residues	573
Excluded volume	77965 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2d2n__assembly_1__model_1`	24-meric （24）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2d2n__assembly_2__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 (7)

Entity 1 Entity 1 polymer

Description description	Giant hemoglobin, A1(b) globin chain
Molecular weight formula_weight	15188.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4452

VCNRLEQILVKTQWAQSYGEAENRAAFSRDLFSELFNIQGSSRALFSGVGVDDMNSAAFTAHCLRVTGALNRLISQLDQQATINADLAHLAGQHASRNLDASNFAAMGQAVMSVVPTHLDCFNQHAWGECYERIASGISG

Entity 2 Entity 2 polymer

Description description	Giant hemoglobin, A2(a5) globin chain
Molecular weight formula_weight	15327.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DCTSLNRLLVKRQWAEAYGEGTNRELLGNRIWEDLFANMPDARGLFSRVNGNDIDSSEFQAHSLRVLGGLDMCVASLDDVPVLNALLARLNSQHDSRGIPAAGYPAFVASAISAVRATVGARSFDNDAWNSCMNQIVSGISG

Entity 3 Entity 3 polymer

Description description	Giant hemoglobin, B2(c) globin chain
Molecular weight formula_weight	15621.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

SSCCSSEDRANVMHNWDAAWSAAYSDRRVALAQAVFASLFSRDAAAQGLFSGVSADNPDSADFRAHCVRVVNGLDVAINMLNDPAVLNEQLAHLSAQHQARAGVAAAHFDVMAEAFAEVMPQVSSCFSSDSWNRCFARIANGISAGL

Entity 4 Entity 4 polymer

Description description	Giant hemoglobin, B1(d) globin chain
Molecular weight formula_weight	14786.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

ECCSRGDAEVVISEWDQVFNAAMAGSSESAVGVAIFDAFFASSGVSPSMFPGGGDSNNPEFLAQVSRVVSGADIAINSLTNRATCDSLLSHLNAQHRAISGVTGAAVTHLSQAISSVVAQVLPSAHIDAWEYCMAYIAAGIGAGL

Entity 5 Entity 5 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 6 Entity 6 non-polymer

Description description	OXYGEN MOLECULE
Molecular weight formula_weight	32.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	METHYL MERCURY ION
Molecular weight formula_weight	215.6 kDa
Source method src_method	syn
Copy count entity_count	4

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2d2nA00
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	2d2nB00
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	2d2nC00
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	2d2nD00
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	111.745 Å
Unit-cell length b length_b	111.745 Å
Unit-cell length c length_c	276.707 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2420
R_free r_free	0.2970

Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi

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

Giant hemoglobin, A1(b) globin chain

State in the Current Structure

Other States of the Same Protein in the Database

Giant hemoglobin, A2(a5) globin chain

State in the Current Structure

Other States of the Same Protein in the Database

Giant hemoglobin, B2(c) globin chain

State in the Current Structure

Other States of the Same Protein in the Database

Giant hemoglobin, B1(d) globin chain

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

2d2n__assembly_2__model_1

2d2n__assembly_2__model_1 | I(q)

2d2n__assembly_2__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)

Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi

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

Giant hemoglobin, A1(b) globin chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Giant hemoglobin, A2(a5) globin chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Giant hemoglobin, B2(c) globin chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Giant hemoglobin, B1(d) globin chain

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

2d2n__assembly_2__model_1

2d2n__assembly_2__model_1 | I(q)

2d2n__assembly_2__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)