6YF3: FKBP12

FKBP12 in complex with the BMP potentiator compound 10 at 1.00A resolution. Determined by X-ray diffraction at 1.0 Å resolution. Released 10 Mar 2021.

Method: X-ray diffraction
Resolution: 1.0 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,090
Mol. weight: 12.97 kDa
Ligands: CD, OOZ
Released: 10 Mar 2021

Explore 6YF3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YF3 contains 5 α-helices and 8 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: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
α-helix	20-21	2
β-strand	22-30	9	1
β-strand	35-38	4	1
β-strand	46-48	3	1
α-helix	57-62	6
α-helix	63-65	3
α-helix	66-67	2
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Peptidyl-prolyl cis-trans isomerase FKBP1A	A	protein	109	Homo sapiens	P62942 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6YF3_1 Peptidyl-prolyl cis-trans isomerase FKBP1A (chains A)
GPGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRG
WEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE

Ligands and cofactors

ID	Name	Formula	Copies
CD	Cadmium ion	Cd	1
OOZ	(1~{R},9~{S},12~{S},13~{R},14~{S},17~{R},18~{E},21~{S},23~{S},24~{R},25~{S},27~…	C42 H67 N O12	1

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

Primary citation

Phenotypic screen identifies calcineurin-sparing FK506 analogs as BMP potentiators for treatment of acute kidney injury. Larraufie, M.H., Gao, X., Xia, X. et al. Cell Chem Biol (2021) 28:1271. DOI 10.1016/j.chembiol.2021.04.001 · 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
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
9DTW 1.39 Å, Co-crystal structure of the ternary complex of human FKBP12, QDPR and Compound 4

Browse structure collections

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