6VCU: Homo sapiens FKBP12 protein

Homo sapiens FKBP12 protein bound with APX879 in P32 space group. Determined by X-ray diffraction at 1.69 Å resolution. Released 16 Dec 2020.

Method: X-ray diffraction
Resolution: 1.69 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,239
Mol. weight: 52.74 kDa
Ligands: R27
Released: 16 Dec 2020

Explore 6VCU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VCU contains 10 α-helices and 32 β-strands across 4 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.

Chains A and B: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	21-30	10	1
β-strand	35-38	4	1
β-strand	46-49	4	1
α-helix	57-63	7
β-strand	71-76	6	1
α-helix	78-80	3
β-strand	87	1	2
β-strand	91	1	2
β-strand	97-106	10	1

Chains C and D: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	5
α-helix	20	1
β-strand	21-30	10	5
β-strand	35-38	4	5
β-strand	46-49	4	5
α-helix	57-63	7
β-strand	71-76	6	5
α-helix	78-80	3
β-strand	87	1	6
β-strand	91	1	6
β-strand	97-106	10	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptidyl-prolyl cis-trans isomerase FKBP1A	A, B, C, D	protein	111	Homo sapiens	P62942 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6VCU_1 Peptidyl-prolyl cis-trans isomerase FKBP1A (chains A, B, C, D)
GSHMGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVI
RGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE

Ligands and cofactors

ID	Name	Formula	Copies
R27	N'-[(3S,4R,5S,8R,9E,12S,14S,15R,16S,18R,19R,26aS)-5,19-dihydroxy-3-{(1E)-1-[(1R…	C46 H73 N3 O12	4

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

Primary citation

Leveraging Fungal and Human Calcineurin-Inhibitor Structures, Biophysical Data, and Dynamics To Design Selective and Nonimmunosuppressive FK506 Analogs. Gobeil, S.M., Bobay, B.G., Juvvadi, P.R. et al. mBio (2021) 12:e0300021-e0300021. DOI 10.1128/mBio.03000-21 · PubMed

Other PDB entries of the same protein (UniProt P62942 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2PPN 0.92 Å, Crystal structure of FKBP12
2PPP 0.94 Å, Crystal structure of E60Q mutant of FKBP12
6YF3 1.0 Å, FKBP12 in complex with the BMP potentiator compound 10 at 1.00A resolution
6YF2 1.03 Å, FKBP12 in complex with the BMP potentiator compound 6 at 1.03A resolution
8X6P 1.05 Å, Isomerase Protein
6YF1 1.12 Å, FKBP12 in complex with the BMP potentiator compound 8 at 1.12A resolution
8CHM 1.12 Å, Human FKBP12 in complex with (1S,5S,6R)-10-((S)-(3,5-dichlorophenyl)sulfinyl)-3-(pyridin-…
4N19 1.2 Å, Structural basis of conformational transitions in the active site and 80 s loop in the…
8PDF 1.2 Å, FKBP12 in complex with PROTAC 6a2
9LYG 1.26 Å, Crystal structure of FKBP12 complexed with Small Molecule Anchor for Protein-201
2PPO 1.29 Å, Crystal structure of E60A mutant of FKBP12
7U8D 1.39 Å, FKBP12 mutant V55G bound to Rapa*-3Z

Browse structure collections

About this viewer

MolViewer shows 6VCU directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.