SAXSdb — 1rod

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

CHIMERIC PROTEIN OF INTERLEUKIN 8 AND HUMAN MELANOMA GROWTH STIMULATING ACTIVITY PROTEIN

Homo sapiens

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 28–80 Chain B； UniProt 28–80	Fragment：INTERLEUKIN 8 RESIDUES 1 - 53, HUMAN MELANOMA GROWTH STIMULATING ACTIVITY PROTEIN RESIDUES 54 - 72	No other associated polymer	SOLUTION NMR mmCIF provides none of the parsed experimental conditions	Resolution not provided

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 1ROD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ICW INTERLEUKIN-8, MUTANT WITH GLU 38 REPLACED BY CYS AND CYS 50 REPLACED BY ALA Deposited 1996-09-18	Different construct Different mutation/modification Different experimental method Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–99（72 aa） Chain B 28–99（72 aa）	Mutation：E38C, C50A Mutation：E38C, C50A	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.01 Å R-free 0.266
1IKL NMR study of monomeric human interleukin-8 (minimized average structure) Deposited 1995-08-03	Different construct Different mutation/modification Different oligomeric state	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–99（72 aa）	Mutation：DEL(1-3), H LEU 25 MODIFIED TO N-METHYL Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1IKM NMR study of monomeric human interleukin-8 (30 structures) Deposited 1995-08-03	Different construct Different mutation/modification Different oligomeric state	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–99（72 aa）	Mutation：DEL(1-3), THE AMIDE PROTON OF LEU 25 MODIFIED TO N-METHYL Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1IL8 THREE-DIMENSIONAL STRUCTURE OF INTERLEUKIN 8 IN SOLUTION Deposited 1990-03-08	Different construct	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–99（72 aa） Chain B 28–99（72 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1ILP CXCR-1 N-TERMINAL PEPTIDE BOUND TO INTERLEUKIN-8 Deposited 1998-12-16	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 28–99（72 aa） Chain B 28–99（72 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；308 K；Ionic strength (raw mmCIF value) 0.15 M；Pressure 1	Resolution not provided
1ILQ CXCR-1 N-TERMINAL PEPTIDE BOUND TO INTERLEUKIN-8 (MINIMIZED MEAN) Deposited 1998-12-17	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 28–99（72 aa） Chain B 28–99（72 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；308 K；Ionic strength (raw mmCIF value) 0.15 M；Pressure 1	Resolution not provided
1QE6 INTERLEUKIN-8 WITH AN ADDED DISULFIDE BETWEEN RESIDUES 5 AND 33 (L5C/H33C) Deposited 1999-07-13	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–99（72 aa） Chain B 28–99（72 aa）	Mutation：L5C, H33C Mutation：L5C, H33C	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；292 K；NACL, AMMONIUM SULFATE, PEG 8000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 19K	Resolution 2.35 Å R-free 0.278
1QE6 INTERLEUKIN-8 WITH AN ADDED DISULFIDE BETWEEN RESIDUES 5 AND 33 (L5C/H33C) Deposited 1999-07-13	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 28–99（72 aa） Chain D 28–99（72 aa）	Mutation：L5C, H33C Mutation：L5C, H33C	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；292 K；NACL, AMMONIUM SULFATE, PEG 8000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 19K	Resolution 2.35 Å R-free 0.278
1QE6 INTERLEUKIN-8 WITH AN ADDED DISULFIDE BETWEEN RESIDUES 5 AND 33 (L5C/H33C) Deposited 1999-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 28–99（72 aa） Chain B 28–99（72 aa） Chain C 28–99（72 aa） Chain D 28–99（72 aa）	Mutation：L5C, H33C Mutation：L5C, H33C Mutation：L5C, H33C Mutation：L5C, H33C	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；292 K；NACL, AMMONIUM SULFATE, PEG 8000, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 19K	Resolution 2.35 Å R-free 0.278
2IL8 THREE-DIMENSIONAL STRUCTURE OF INTERLEUKIN 8 IN SOLUTION Deposited 1990-03-08	Different construct	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–99（72 aa） Chain B 28–99（72 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
3IL8 CRYSTAL STRUCTURE OF INTERLEUKIN 8: SYMBIOSIS OF NMR AND CRYSTALLOGRAPHY Deposited 1990-12-07	Different construct Different mutation/modification Different experimental method Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–99（72 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
4XDX The crystal structure of soluble human interleukin 8 expressed in Pichia pastoris Deposited 2014-12-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–99（70 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；0.17 M Ammonium acetate, 0.085 M Sodium citrate tribasic dihydrate pH 5.6, 20% w/v Polyethylene glycol 4,000, 15% v/v Glycerol	Resolution 0.95 Å R-free 0.136
5D14 The atomic resolution crystal structure of human IL-8 Deposited 2015-08-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–99（70 aa） Fragment：unp residues 30-99	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；291 K；0.17 M Ammonium acetate, 0.085 M Sodium citrate tribasic dihydrate pH 5.6, 20% w/v Polyethylene glycol 4,000, 15% v/v Glycerol. All crystals were grown at 18 deg C.	Resolution 1.00 Å R-free 0.135
5WDZ Structure of monomeric Interleukin-8 (1-66) Deposited 2017-07-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–93（66 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.3；313 K；Ionic strength (raw mmCIF value) 20；Pressure 1 NMR sample composition 20 mM [U-13C; U-15N] IL-8 1-66, 20 mM HEPES, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 20 mM [U-15N] IL-8, 20 mM HEPES, 70 mM sodium chloride, 13.5 mg/L Y21M bacteriophage, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 20 mM [U-15N] IL-8 1-66, 20 mM HEPES, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6LFM Cryo-EM structure of a class A GPCR Deposited 2019-12-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain D 28–99（72 aa） Chain E 28–99（72 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
6LFO Cryo-EM structure of a class A GPCR monomer Deposited 2019-12-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 28–92（65 aa）	Not recorded	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6N2U IL-8 Structure from Bacterial Expression Source Deposited 2018-11-14	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–99（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2.4 M Ammonium Phosphate dibasic, 0.1 M Tris HCl pH 8.5	Resolution 1.25 Å R-free 0.223
6WZM LY3041658 Fab bound to CXCL8 Deposited 2020-05-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 28–93（66 aa） Chain F 28–93（66 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；20% PEG 3350, 200mM Magnesium Chloride	Resolution 2.28 Å R-free 0.229
6XMN Solution NMR CXCL8-CXCR1 N-domain complex structure Deposited 2020-06-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–93（66 aa） Fragment：residues 28-93	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 0.4 mM [U-13C; U-15N] CXCL8, 1.2 mM CXCR1, 50 mM sodium phosphate, 0.01 % sodium azide, 10 % [U-100% 2H] D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.2 mM CXCL8, 0.5 mM [U-13C; U-15N] CXCR1, 50 mM sodium phosphate, 0.01 % sodium azide, 10 % [U-100% 2H] D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
8IC0 Cryo-EM structure of CXCL8 bound C-X-C chemokine receptor 1 in complex with Gi heterotrimer Deposited 2023-02-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 28–99（72 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50 mM HEPES pH8.0, 100 mM NaCl, 1 mM MgCl2, 0.5 mM TCEP, 0.001% LMNG, 0.0001% CHS, 1 uM IL8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.41 Å
8XWN Structure of CXCR2 bound to CXCL8 (Ligand-receptor focused map) Deposited 2024-01-16	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 21–99（79 aa） Chain E 21–99（79 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
8XX6 Structure of CXCR2 bound to CXCL8 (CXCR2-CXCL8-Go Full map) Deposited 2024-01-17	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain D 21–99（79 aa） Chain E 21–99（79 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.99 Å
8YNF Structure of Duffy Antigen Receptor for Chemokines (DARC)/ACKR1 in complex with the chemokine, CXCL8 Deposited 2024-03-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 21–99（79 aa） Chain E 21–99（79 aa） Chain G 21–99（79 aa） Chain H 21–99（79 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.65 Å

21 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IL8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–53； UniProt 28–80 Author chain B； PDBConstruct 1–53； UniProt 28–80

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	1rod
Deposition date deposition_date	1995-11-24
Structure title title	CHIMERIC PROTEIN OF INTERLEUKIN 8 AND HUMAN MELANOMA GROWTH STIMULATING ACTIVITY PROTEIN, NMR
Keywords keywords	CYTOKINE, CHEMOTAXIS, INFLAMMATORY RESPONSE, CHEMOKINE; CHEMOKINE
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	17.86 Å
Radius of gyration Rg (electron density) rg_electron	16.92 Å
Forward intensity I(0) i0	236795000.00
Molecular weight molecular_weight	130310.0 kDa
Excluded volume excluded_volume	164800 Å³
Envelope volume envelope_volume	51453 Å³
Hydration-shell volume shell_volume	20892 Å³
Envelope diameter envelope_diameter	72.4 Å
Shell Rg shell_rg	27.49 Å
Envelope Rg envelope_rg	21.58 Å
Shape Rg shape_rg	16.88 Å
Total Rg total_rg	17.55 Å
Total atoms total_atoms	18640
Residues n_residues	1152
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	67.9 Å
Rg (real space) rg_real	17.96 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	2.3680e+08
I(0) uncertainty (real space) i0_real_error	3.2630e+06
Rg (reciprocal space) rg_reciprocal	17.95 Å
I(0) (reciprocal space) i0_reciprocal	236800000.0000
Solution quality estimate total_estimate	0.7291
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.0 Å
Skewness Skewness skewness	0.521
Kurtosis Kurtosis kurtosis	0.114
Angular range angular_range	— – 0.4450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	952200.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.573; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.764; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1roda_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

Domain ID domain_id	d1rodb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

CATH v4.4 (2 domains)

Domain ID domain_id	1rodA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1rodB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	CHIMERIC PROTEIN OF INTERLEUKIN 8 AND HUMAN MELANOMA GROWTH STIMULATING ACTIVITY PROTEIN
Molecular weight formula_weight	8155.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	18640

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

CHIMERIC PROTEIN OF INTERLEUKIN 8 AND HUMAN MELANOMA GROWTH STIMULATING ACTIVITY PROTEIN, NMR

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

CHIMERIC PROTEIN OF INTERLEUKIN 8 AND HUMAN MELANOMA GROWTH STIMULATING ACTIVITY PROTEIN

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/ro/1rod/1rod.fit
pddf	/app/data/pr_computation/ro/1rod/1rod.pr.out
profile	/app/data/saxs_computation/ro/1rod/1rod.dat