6qba

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

Method: X-RAY DIFFRACTION

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA-binding protein 7a × 1 （P61991） 2-[({4-[2-(trifluoromethyl)phenyl]piperidin-1-yl}carbonyl)amino]benzoic acid × 1 IMIDAZOLE × 5 DI(HYDROXYETHYL)ETHER × 1 ZINC ION × 3 ACETATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Retinol-binding protein 4 × 1 （P02753） 2-[({4-[2-(trifluoromethyl)phenyl]piperidin-1-yl}carbonyl)amino]benzoic acid × 1 IMIDAZOLE × 5 DI(HYDROXYETHYL)ETHER × 1 ZINC ION × 3 ACETATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

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. 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.

6qba__assembly_1__model_1

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

Download this curve (.dat)

6qba__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6qba__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.58 Å
Rg (electron density)	19.73 Å
Total Rg	20.79 Å
Atom count	3849
Residues	237
Excluded volume	34752 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6qba__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 (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

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism 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

Source Source

Source organism organism	Sulfolobus solfataricus
NCBI taxonomy ID ncbi_taxonomy_id	2287
Host organism 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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6. 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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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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6qba__assembly_1__model_1

6qba__assembly_1__model_1 | I(q)

6qba__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-binding protein 7a

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

6qba__assembly_1__model_1

6qba__assembly_1__model_1 | I(q)

6qba__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)