SAXSdb — 6qba

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

Retinol-binding protein 4

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 19–201	Not recorded	DNA-binding protein 7a × 1 （P61991） 2T1 2-[({4-[2-(trifluoromethyl)phenyl]piperidin-1-yl}carbonyl)amino]benzoic acid × 1 IMD IMIDAZOLE × 5 PEG DI(HYDROXYETHYL)ETHER × 1 ZN ZINC ION × 3 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295.15 K；0.2 M Zn acetate 0.1 M imidazole pH 8 20% PEG 3K	Resolution 1.80 Å R-free 0.221

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 6QBA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BRP CRYSTAL STRUCTURE OF THE TRIGONAL FORM OF HUMAN PLASMA RETINOL-BINDING PROTEIN AT 2.5 ANGSTROMS RESOLUTION Deposited 1992-07-27	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 17–198（182 aa）	Not recorded	RTL RETINOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1BRQ CRYSTAL STRUCTURE OF THE TRIGONAL FORM OF HUMAN PLASMA RETINOL-BINDING PROTEIN AT 2.5 ANGSTROMS RESOLUTION Deposited 1992-07-27	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 17–198（182 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1JYD Crystal Structure of Recombinant Human Serum Retinol-Binding Protein at 1.7 A Resolution Deposited 2001-09-12	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 17–198（182 aa）	Not recorded	GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；289 K；Sodium cacodylate, sodium chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.70 Å R-free 0.270
1JYJ Crystal Structure of a Double Variant (W67L/W91H) of Recombinant Human Serum Retinol-binding Protein at 2.0 A Resolution Deposited 2001-09-12	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 17–198（182 aa）	Mutation：W67L, W91H	GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.1；289 K；Sodium Chloride, Tris/HCl buffer, beta-octyl-glucoside, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.00 Å R-free 0.229
1QAB The structure of human retinol binding protein with its carrier protein transthyretin reveals interaction with the carboxy terminus of RBP Deposited 1999-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 24–201（178 aa） Chain F 24–201（178 aa）	Not recorded	RTL RETINOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.403
1RBP CRYSTALLOGRAPHIC REFINEMENT OF HUMAN SERUM RETINOL BINDING PROTEIN AT 2 ANGSTROMS RESOLUTION Deposited 1990-04-02	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 17–198（182 aa）	Not recorded	RTL RETINOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1RLB RETINOL BINDING PROTEIN COMPLEXED WITH TRANSTHYRETIN Deposited 1995-02-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 17–190（174 aa） Chain F 17–190（174 aa）	Not recorded	REA RETINOIC ACID × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.10 Å
2WQ9 Crystal Structure of RBP4 bound to Oleic Acid Deposited 2009-08-14	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 19–192（174 aa） Fragment：RESIDUES 19-192	Not recorded	CL CHLORIDE ION × 5 OLA OLEIC ACID × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions 3.5 TO 4.2 M NACL, 1M HEPES PH 7.2	Resolution 1.65 Å R-free 0.219
2WQA Complex of TTR and RBP4 and Oleic Acid Deposited 2009-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 19–194（176 aa） Chain F 19–194（176 aa）	Not recorded	SO4 SULFATE ION × 11 OLA OLEIC ACID × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.85 Å R-free 0.253
2WR6 Structure of the complex of RBP4 with linoleic acid Deposited 2009-08-29	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 19–192（174 aa） Fragment：RESIDUES 19-192	Not recorded	CL CHLORIDE ION × 1 ODT (11E,13E,15Z)-OCTADECA-11,13,15-TRIENOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions 3.5-4.2M NACL, 0.1M HEPES, PH 7.2	Resolution 1.80 Å R-free 0.227
3BSZ Crystal structure of the transthyretin-retinol binding protein-Fab complex Deposited 2007-12-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain E 19–194（176 aa） Chain F 19–194（176 aa）	Not recorded	RTL RETINOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；2.35M ammonium phosphate, 10mM sodium citrate, 10mM beta-mercaptoethanol, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.38 Å R-free 0.312
3FMZ Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with non-retinoid ligand Deposited 2008-12-22	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 19–201（183 aa）	Not recorded	2T1 2-[({4-[2-(trifluoromethyl)phenyl]piperidin-1-yl}carbonyl)amino]benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；289 K；0.4M Mg formate, 0.1M GndHCl, 0.1M Bis-Tris 6.5, vapor diffusion, temperature 289K	Resolution 2.90 Å R-free 0.286
3FMZ Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with non-retinoid ligand Deposited 2008-12-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 19–201（183 aa）	Not recorded	2T1 2-[({4-[2-(trifluoromethyl)phenyl]piperidin-1-yl}carbonyl)amino]benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；289 K；0.4M Mg formate, 0.1M GndHCl, 0.1M Bis-Tris 6.5, vapor diffusion, temperature 289K	Resolution 2.90 Å R-free 0.286
4O9S Crystal structure of Retinol-Binding Protein 4 (RBP4)in complex with a non-retinoid ligand Deposited 2014-01-02	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 19–201（183 aa）	Not recorded	2RY 1-[4-(7-thia-9,11-diazatricyclo[6.4.0.0^{2,6}]dodeca-1(12),2(6),8,10-tetraen-12-yl)piperazin-1-yl]-2-[2-(trifluoromethyl)phenyl]ethanone × 1 EDO 1,2-ETHANEDIOL × 13 CL CHLORIDE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；1M ammonium phosphate dibasic, 0.1M imidazole, 0.2M sodium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.30 Å R-free 0.261
4O9S Crystal structure of Retinol-Binding Protein 4 (RBP4)in complex with a non-retinoid ligand Deposited 2014-01-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 19–201（183 aa）	Not recorded	2RY 1-[4-(7-thia-9,11-diazatricyclo[6.4.0.0^{2,6}]dodeca-1(12),2(6),8,10-tetraen-12-yl)piperazin-1-yl]-2-[2-(trifluoromethyl)phenyl]ethanone × 1 EDO 1,2-ETHANEDIOL × 13 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；1M ammonium phosphate dibasic, 0.1M imidazole, 0.2M sodium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.30 Å R-free 0.261
4O9S Crystal structure of Retinol-Binding Protein 4 (RBP4)in complex with a non-retinoid ligand Deposited 2014-01-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 19–201（183 aa） Chain B 19–201（183 aa）	Not recorded	2RY 1-[4-(7-thia-9,11-diazatricyclo[6.4.0.0^{2,6}]dodeca-1(12),2(6),8,10-tetraen-12-yl)piperazin-1-yl]-2-[2-(trifluoromethyl)phenyl]ethanone × 2 EDO 1,2-ETHANEDIOL × 26 CL CHLORIDE ION × 3 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；1M ammonium phosphate dibasic, 0.1M imidazole, 0.2M sodium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.30 Å R-free 0.261
4PSQ Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with a non-retinoid ligand Deposited 2014-03-07	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 B 19–201（183 aa） Fragment：UNP residues 19-201	Not recorded	2WL (1-benzyl-1H-imidazol-4-yl)[4-(2-chlorophenyl)piperazin-1-yl]methanone × 1 PO4 PHOSPHATE ION × 1 EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1 M ammonium phosphate dibasic, 0.1 M imidazole, pH 8.0, 200 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.40 Å R-free 0.287
4PSQ Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with a non-retinoid ligand Deposited 2014-03-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–201（183 aa） Fragment：UNP residues 19-201	Not recorded	2WL (1-benzyl-1H-imidazol-4-yl)[4-(2-chlorophenyl)piperazin-1-yl]methanone × 1 PO4 PHOSPHATE ION × 1 EDO 1,2-ETHANEDIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1 M ammonium phosphate dibasic, 0.1 M imidazole, pH 8.0, 200 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.40 Å R-free 0.287
5NTY Structure of non-fluorescent human plasma RBP4 Deposited 2017-04-28	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 19–200（182 aa）	Not recorded	PLM PALMITIC ACID × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；279 K；4.5M NaCl, 20mM Na cacodylate, pH 6.8	Resolution 2.00 Å R-free 0.230
5NU2 Structure of non-fluorescent human urine RBP4 Deposited 2017-04-28	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 19–200（182 aa）	Not recorded	PLM PALMITIC ACID × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；4.3 M NaCl, 100 mM Hepes, pH 7.5	Resolution 1.50 Å R-free 0.184
5NU6 Structure of non-fluorescent human amniotic fluid RBP4 Deposited 2017-04-28	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 19–200（182 aa）	Not recorded	PLM PALMITIC ACID × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；4.3 M NaCl, 100 mM Hepes, pH 7.5	Resolution 1.68 Å R-free 0.197
5NU7 Structure of human holo plasma RBP4 Deposited 2017-04-28	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 19–200（182 aa）	Not recorded	RTL RETINOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；277 K；4.5 M NaCl, 20 mM Na cacodylate, pH 6.8	Resolution 1.50 Å R-free 0.210
5NU8 Structure of human urine RBP4 saturated with palmitate Deposited 2017-04-28	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 19–200（182 aa）	Not recorded	PLM PALMITIC ACID × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；4.3 M NaCl, 100 mM Hepes, pH 7.5	Resolution 1.59 Å R-free 0.212
5NU9 Structure of human amniotic fluid RBP4 saturated with palmitate Deposited 2017-04-28	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 19–200（182 aa）	Not recorded	PLM PALMITIC ACID × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；4.3 M NaCl, 100 mM Hepes, pH 7.5	Resolution 1.50 Å R-free 0.195
5NUA Structure of human urine RBP4 saturated with laurate Deposited 2017-04-28	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 19–200（182 aa）	Not recorded	DAO LAURIC ACID × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；4.3 M NaCl, 100 mM Hepes, pH 7.5	Resolution 1.60 Å R-free 0.197
5NUB Structure of human amniotic fluid RBP4 saturated with laurate Deposited 2017-04-28	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 19–200（182 aa）	Not recorded	DAO LAURIC ACID × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；4.3 M NaCl, 100 mM Hepes, pH 7.5	Resolution 1.60 Å R-free 0.205

22 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RET4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–185； UniProt 19–201

DNA-binding protein 7a

Sulfolobus solfataricus

UniProt P61991

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 2–62	Not recorded	Retinol-binding protein 4 × 1 （P02753） 2T1 2-[({4-[2-(trifluoromethyl)phenyl]piperidin-1-yl}carbonyl)amino]benzoic acid × 1 IMD IMIDAZOLE × 5 PEG DI(HYDROXYETHYL)ETHER × 1 ZN ZINC ION × 3 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295.15 K；0.2 M Zn acetate 0.1 M imidazole pH 8 20% PEG 3K	Resolution 1.80 Å R-free 0.221

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 6QBA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B4O NMR STUDY OF SSO7D MUTANT (F31A) MINIMIZED AVERAGE STRUCTURE Deposited 1998-12-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–62（62 aa）	Mutation：F31A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；300 K NMR sample composition H2O	Resolution not provided
1SSO SOLUTION STRUCTURE AND DNA-BINDING PROPERTIES OF A THERMOSTABLE PROTEIN FROM THE ARCHAEON SULFOLOBUS SOLFATARICUS Deposited 1995-03-31	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–62（62 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2CVR NMR solution structure of sso7d mutant, K12L, 12 conformers Deposited 2005-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–62（62 aa）	Mutation：K12L	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；300 K；Pressure AMBIENT NMR sample composition 2mM K12L; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 2mM K12L; 100% D2O \| 100% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	DN7A_SULSO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–61； UniProt 2–62

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	6qba
Deposition date deposition_date	2018-12-20
Structure title title	Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with non-retinoid ligand A1120 and engineered binding scaffold
Keywords keywords	Lipocalin, RBP4, Retinol binding protein, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	20.58 Å
Radius of gyration Rg (electron density) rg_electron	19.73 Å
Forward intensity I(0) i0	15122300.00
Molecular weight molecular_weight	28183.0 kDa
Excluded volume excluded_volume	34752 Å³
Envelope volume envelope_volume	41254 Å³
Hydration-shell volume shell_volume	18054 Å³
Envelope diameter envelope_diameter	72.4 Å
Shell Rg shell_rg	25.75 Å
Envelope Rg envelope_rg	20.28 Å
Shape Rg shape_rg	19.66 Å
Total Rg total_rg	20.79 Å
Total atoms total_atoms	3849
Residues n_residues	237
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	68.9 Å
Rg (real space) rg_real	20.62 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	1.5120e+07
I(0) uncertainty (real space) i0_real_error	2.0460e+05
Rg (reciprocal space) rg_reciprocal	20.61 Å
I(0) (reciprocal space) i0_reciprocal	15120000.0000
Solution quality estimate total_estimate	0.7958
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.0 Å
Skewness Skewness skewness	0.428
Kurtosis Kurtosis kurtosis	-0.259
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3799000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.791; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Retinol-binding protein 4
Molecular weight formula_weight	21251.8 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	4058

GPERDCRVSSFRVKENFDKARFSGTWYAMAKKDPEGLFLQDNIVAEFSVDETGQMSATAKGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWGVASFLQKGNDDHWIVDTDYDTYAVQYSCRLLNLDGTCADSYSFVFSRDPNGLPPEAQKIVRQRQEELCLARQYRLIVHNGYCDGRSERNLL

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	Komagataella pastoris

Entity 2 Entity 2 polymer

Description description	DNA-binding protein 7a
Molecular weight formula_weight	6930.7 kDa
EC 编号 ec_number	3.1.27.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ATVKLTYQGEEKQVDISKIKRVARYGQNIYFSYDEGGGAYDYGAVSEKDAPKELLQMLEKQ

来源 Source

来源生物 organism	Sulfolobus solfataricus
NCBI Class编号 ncbi_taxonomy_id	2287
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	2-[({4-[2-(trifluoromethyl)phenyl]piperidin-1-yl}carbonyl)amino]benzoic acid
Molecular weight formula_weight	392.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	209

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6qbaa_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.1 — Retinol binding protein-like

Domain ID domain_id	d6qbab_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.13 — Chromo domain-like
Family Family family	b.34.13.1 — Histone-like proteins from archaea

CATH v4.4 (1 domains)

Domain ID domain_id	6qbaA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

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8. Citations (1)

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Unit-cell length a length_a	44.456 Å
Unit-cell length b length_b	77.614 Å
Unit-cell length c length_c	80.509 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	40.250 Å
R factor r_factor	0.1901
R_work r_work	0.1881
R_free r_free	0.2207

fit	/app/data/saxs_computation/qb/6qba/6qba.fit
pddf	/app/data/pr_computation/qb/6qba/6qba.pr.out
profile	/app/data/saxs_computation/qb/6qba/6qba.dat

Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with non-retinoid ligand A1120 and engineered binding scaffold

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

Retinol-binding protein 4

State in the Current Structure

Other States of the Same Protein in the Database

DNA-binding protein 7a

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)