3FMZ: Retinol-Binding Protein 4

Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with non-retinoid ligand. Determined by X-ray diffraction at 2.9 Å resolution. Released 27 Jan 2009.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,881
Mol. weight: 50.03 kDa
Ligands: 2T1
Released: 27 Jan 2009

Explore 3FMZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3FMZ contains 7 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: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	17-20	4
β-strand	22-30	9	1
β-strand	39-47	9	1
β-strand	53-63	11	1
β-strand	67-78	12	1
β-strand	85-92	8	1
β-strand	99-109	11	1
β-strand	114-123	10	1
β-strand	129-138	10	1
α-helix	146-158	13
β-strand	166-167	2	1

Chain B: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	2
α-helix	6-8	3
α-helix	17-20	4
β-strand	22-30	9	3
β-strand	39-47	9	3
β-strand	53-62	10	3
β-strand	68-79	12	3
β-strand	85-92	8	3
β-strand	99-109	11	3
β-strand	114-118	5	3
β-strand	119-123	5	4
β-strand	128	1	2
β-strand	129-133	5	4
β-strand	134-138	5	3
α-helix	146-159	14
β-strand	166-167	2	3
α-helix	168-169	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinol-binding protein 4	A, B	protein	212	Homo sapiens	P02753 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3FMZ_1 Retinol-binding protein 4 (chains A, B)
MASMSYYHHHHHHDYDIPTTENLYFQGAMERDCRVSSFRVKENFDKARFSGTWYAMAKKD
PEGLFLQDNIVAEFSVDETGQMSATAKGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYW
GVASFLQKGNDDHWIVDTDYDTYAVQYSCRLLNLDGTCADSYSFVFSRDPNGLPPEAQKI
VRQRQEELCLARQYRLIVHNGYCDGRSERNLL

Ligands and cofactors

ID	Name	Formula	Copies
2T1	2-[({4-[2-(trifluoromethyl)phenyl]piperidin-1-yl}carbonyl)amino]benzoic acid	C20 H19 F3 N2 O3	2

Primary citation

Identification and Characterization of a Non-retinoid Ligand for Retinol-binding Protein 4 Which Lowers Serum Retinol-binding Protein 4 Levels in Vivo. Motani, A., Wang, Z., Conn, M. et al. J Biol Chem (2009) 284:7673-7680. DOI 10.1074/jbc.M809654200 · 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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