5NU9: Retinol-binding protein 4

Structure of human amniotic fluid RBP4 saturated with palmitate. Determined by X-ray diffraction at 1.5 Å resolution. Released 7 Mar 2018.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,538
Mol. weight: 21.31 kDa
Ligands: PLM
Released: 7 Mar 2018

Explore 5NU9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5NU9 contains 4 α-helices and 11 β-strands across 1 chain. 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: 4 helices, 11 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	67-79	13	1
β-strand	85-92	8	1
β-strand	100-109	10	1
β-strand	114-118	5	1
β-strand	119-123	5	2
β-strand	129-133	5	2
β-strand	134-138	5	1
α-helix	146-158	13
β-strand	166-167	2	1
α-helix	168-169	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Retinol-binding protein 4	A	protein	182	Homo sapiens	P02753 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5NU9_1 Retinol-binding protein 4 (chains A)
ERDCRVSSFRVKENFDKARFSGTWYAMAKKDPEGLFLQDNIVAEFSVDETGQMSATAKGR
VRLLNNWDVCADMVGTFTDTEDPAKFKMKYWGVASFLQKGNDDHWIVDTDYDTYAVQYSC
RLLNLDGTCADSYSFVFSRDPNGLPPEAQKIVRQRQEELCLARQYRLIVHNGYCDGRSER
NL

Ligands and cofactors

ID	Name	Formula	Copies
PLM	Palmitic acid	C16 H32 O2	1

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

Primary citation

Human plasma retinol-binding protein (RBP4) is also a fatty acid-binding protein. Perduca, M., Nicolis, S., Mannucci, B. et al. Biochim Biophys Acta (2018) 1863:458-466. DOI 10.1016/j.bbalip.2018.01.010 · 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
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…
1RBP 2.0 Å, Crystallographic refinement of human serum retinol binding protein at 2 Å resolution

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