4O9S: Retinol-binding protein 4

Crystal structure of Retinol-Binding Protein 4 (RBP4)in complex with a non-retinoid ligand. Determined by X-ray diffraction at 2.3 Å resolution. Released 2 Jul 2014.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,235
Mol. weight: 52.64 kDa
Ligands: 2RY
Released: 2 Jul 2014

Explore 4O9S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4O9S contains 5 α-helices and 22 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
α-helix	17-20	4
β-strand	22-30	9	2
β-strand	39-47	9	2
β-strand	53-62	10	2
β-strand	68-79	12	2
β-strand	85-92	8	2
β-strand	99-109	11	2
β-strand	114-123	10	2
β-strand	128	1	1
β-strand	129-138	10	2
α-helix	146-158	13
β-strand	166-167	2	2

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	3
α-helix	6-8	3
α-helix	17-20	4
β-strand	22-30	9	4
β-strand	39-47	9	4
β-strand	53-64	12	4
β-strand	67-79	13	4
β-strand	85-92	8	4
β-strand	99-109	11	4
β-strand	114-123	10	4
β-strand	128	1	3
β-strand	129-138	10	4
α-helix	146-158	13
β-strand	166-167	2	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinol-binding protein 4	A, B	protein	215	Homo sapiens	P02753 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4O9S_1 Retinol-binding protein 4 (chains A, B)
HISMASMSYYHHHHHHDYDIPTTENLYFQGAMERDCRVSSFRVKENFDKARFSGTWYAMA
KKDPEGLFLQDNIVAEFSVDETGQMSATAKGRVRLLNNWDVCADMVGTFTDTEDPAKFKM
KYWGVASFLQKGNDDHWIVDTDYDTYAVQYSCRLLNLDGTCADSYSFVFSRDPNGLPPEA
QKIVRQRQEELCLARQYRLIVHNGYCDGRSERNLL

Ligands and cofactors

ID	Name	Formula	Copies
2RY	1-[4-(7-thia-9,11-diazatricyclo[6.4.0.0^{2,6}]dodeca-1(12),2(6),8,10-tetraen-12…	C22 H21 F3 N4 O S	2

Water and common crystallization additives (PEG, CL, EDO) are not listed.

Primary citation

Structure-assisted discovery of the first non-retinoid ligands for Retinol-Binding Protein 4. Wang, Y., Connors, R., Fan, P. et al. Bioorg Med Chem Lett (2014) 24:2885-2891. DOI 10.1016/j.bmcl.2014.04.089 · PubMed

Other PDB entries of the same protein (UniProt P02753 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NU2 1.5 Å, Structure of non-fluorescent human urine RBP4
5NU7 1.5 Å, Structure of human holo plasma RBP4
5NU9 1.5 Å, Structure of human amniotic fluid RBP4 saturated with palmitate
5NU8 1.59 Å, Structure of human urine RBP4 saturated with palmitate
5NUA 1.6 Å, Structure of human urine RBP4 saturated with laurate
5NUB 1.6 Å, Structure of human amniotic fluid RBP4 saturated with laurate
2WQ9 1.65 Å, Crystal Structure of RBP4 bound to Oleic Acid
5NU6 1.68 Å, Structure of non-fluorescent human amniotic fluid RBP4
1JYD 1.7 Å, Crystal Structure of Recombinant Human Serum Retinol-Binding Protein at 1.7 A Resolution
2WR6 1.8 Å, Structure of the complex of RBP4 with linoleic acid
6QBA 1.8 Å, Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with non-retinoid…
1JYJ 2.0 Å, Crystal Structure of a Double Variant (W67L/W91H) of Recombinant Human Serum…

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