SAXSdb — 2igf

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

PEPTIDE (RESIDUES 69-87 OF MYOHEMERYTHRIN)

OrganismNot specified

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain P； UniProt 69–87	Not recorded	IGG1-KAPPA B13I2 FAB (LIGHT CHAIN) × 1 IGG1-KAPPA B13I2 FAB (HEAVY CHAIN) × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.80 Å
2	Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain P； UniProt 69–87	Not recorded	IGG1-KAPPA B13I2 FAB (LIGHT CHAIN) × 2 IGG1-KAPPA B13I2 FAB (HEAVY CHAIN) × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.80 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 2IGF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A7D CHLOROMET MYOHEMERYTHRIN FROM THEMISTE ZOSTERICOLA Deposited 1998-03-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–118（118 aa）	Not recorded	CL CHLORIDE ION × 2 CFO CHLORO DIIRON-OXO MOIETY × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；27% PEG 6K, 100MM HEPES, 1.0M LICL (PH 7.0)	Resolution 1.80 Å R-free 0.227
1A7E HYDROXOMET MYOHEMERYTHRIN FROM THEMISTE ZOSTERICOLA Deposited 1998-03-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–118（118 aa）	Mutation：L103N	CL CHLORIDE ION × 2 OFO HYDROXY DIIRON-OXO MOIETY × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；27% PEG 6K, 100MM HEPES, 1.0M LICL (PH 7.0)	Resolution 1.80 Å R-free 0.227
2MHR STRUCTURE OF MYOHEMERYTHRIN IN THE AZIDOMET STATE AT 1.7(SLASH)1.3 ANGSTROMS RESOLUTION Deposited 1987-04-20	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–118（118 aa）	Not recorded	AZI AZIDE ION × 1 SO4 SULFATE ION × 3 FEO MU-OXO-DIIRON × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.30 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HEMM_THEZO
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain P； PDBConstruct 1–19； UniProt 69–87

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	2igf
Deposition date deposition_date	1991-03-21
Structure title title	CRYSTAL STRUCTURES OF AN ANTIBODY TO A PEPTIDE AND ITS COMPLEX WITH PEPTIDE ANTIGEN AT 2.8 ANGSTROMS
Keywords keywords	IMMUNOGLOBULIN; IMMUNOGLOBULIN
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	26.13 Å
Radius of gyration Rg (electron density) rg_electron	25.02 Å
Forward intensity I(0) i0	41104400.00
Molecular weight molecular_weight	48865.0 kDa
Excluded volume excluded_volume	60815 Å³
Envelope volume envelope_volume	75760 Å³
Hydration-shell volume shell_volume	25493 Å³
Envelope diameter envelope_diameter	82.6 Å
Shell Rg shell_rg	32.02 Å
Envelope Rg envelope_rg	24.65 Å
Shape Rg shape_rg	24.98 Å
Total Rg total_rg	25.91 Å
Total atoms total_atoms	3436
Residues n_residues	436
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	80.3 Å
Rg (real space) rg_real	26.11 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	4.1100e+07
I(0) uncertainty (real space) i0_real_error	5.2670e+05
Rg (reciprocal space) rg_reciprocal	26.12 Å
I(0) (reciprocal space) i0_reciprocal	41100000.0000
Solution quality estimate total_estimate	0.9075
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.6 Å
Skewness Skewness skewness	0.269
Kurtosis Kurtosis kurtosis	-0.570
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7535000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.885

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	IGG1-KAPPA B13I2 FAB (LIGHT CHAIN)
Molecular weight formula_weight	24148.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	3436

DVLMTQTPLSLPVSLGDQASISCRSNQTILLSDGDTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090

Entity 2 Entity 2 polymer

Description description	IGG1-KAPPA B13I2 FAB (HEAVY CHAIN)
Molecular weight formula_weight	23807.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVQLVESGGDLVKPGGSLKLSCAASGFTFSRCAMSWVRQTPEKRLEWVAGISSGGSYTFYPDTVKGRFIISRNNARNTLSLQMSSLRSEDTAIYYCTRYSSDPFYFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090

Entity 3 Entity 3 polymer

Description description	PEPTIDE (RESIDUES 69-87 OF MYOHEMERYTHRIN)
Molecular weight formula_weight	2211.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

EVVPHKKMHKDFLEKIGGL

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2igfh1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2igfh2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2igfl1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2igfl2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (4 domains)

Domain ID domain_id	2igfH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2igfH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2igfL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2igfL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (2)

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Unit-cell length a length_a	142.500 Å
Unit-cell length b length_b	142.500 Å
Unit-cell length c length_c	101.500 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 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2200
R_free r_free	—

fit	/app/data/saxs_computation/ig/2igf/2igf.fit
pddf	/app/data/pr_computation/ig/2igf/2igf.pr.out
profile	/app/data/saxs_computation/ig/2igf/2igf.dat

CRYSTAL STRUCTURES OF AN ANTIBODY TO A PEPTIDE AND ITS COMPLEX WITH PEPTIDE ANTIGEN AT 2.8 ANGSTROMS

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

PEPTIDE (RESIDUES 69-87 OF MYOHEMERYTHRIN)

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

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)