6LDP: CDK5R1-bound FEM1C

Structure of CDK5R1-bound FEM1C. Determined by X-ray diffraction at 2.35 Å resolution. Released 21 Oct 2020.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,723
Mol. weight: 91.61 kDa
Released: 21 Oct 2020

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

Secondary structure: helices and β-sheets

6LDP contains 53 α-helices and 8 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: 28 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-13	7
α-helix	16-24	9
α-helix	31-35	5
β-strand	39	1	1
β-strand	42	1	1
α-helix	44-50	7
α-helix	54-63	10
α-helix	65-67	3
β-strand	72-76	5	2
β-strand	79-84	6	2
α-helix	86-93	8
α-helix	96-104	9
α-helix	119-125	7
α-helix	129-137	9
α-helix	152-158	7
α-helix	162-170	9
α-helix	185-192	8
α-helix	195-202	8
α-helix	206-208	3
α-helix	217-224	8
α-helix	227-233	7
α-helix	241-254	14
α-helix	255-259	5
α-helix	262-278	17
α-helix	285-287	3
α-helix	294-296	3
α-helix	305-309	5
α-helix	310-313	4
α-helix	315-330	16
α-helix	335-350	16
α-helix	354-369	16
α-helix	386-390	5

Chain B: 25 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	9-12	4
α-helix	18-21	4
α-helix	32-34	3
β-strand	39	1	3
β-strand	42	1	3
α-helix	44-50	7
α-helix	54-61	8
β-strand	72-76	5	4
β-strand	79-84	6	4
α-helix	86-93	8
α-helix	96-104	9
α-helix	119-126	8
α-helix	129-137	9
α-helix	152-159	8
α-helix	162-170	9
α-helix	185-192	8
α-helix	195-203	9
α-helix	206-208	3
α-helix	217-224	8
α-helix	227-233	7
α-helix	241-257	17
α-helix	262-276	15
α-helix	285-287	3
α-helix	305-308	4
α-helix	311-313	3
α-helix	315-330	16
α-helix	335-350	16
α-helix	354-368	15
α-helix	386-389	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein fem-1 homolog C,Peptide from Cyclin-dependent kinase 5 activator 1	A, B	protein	418	Homo sapiens	Q15078 (AlphaFold model), Q96JP0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6LDP_1 Protein fem-1 homolog C,Peptide from Cyclin-dependent kinase 5 activator 1 (chains A, B)
GHMDLKTAVFNAARDGKLRLLTKLLASKSKEEVSSLISEKTNGATPLLMAARYGHLDMVE
FLLEQCSASIEVGGSVNFDGETIEGAPPLWAASAAGHLKVVQSLLNHGASVNNTTLTNST
PLRAACFDGHLEIVKYLVEHKADLEVSNRHGHTCLMISCYKGHKEIAQYLLEKGADVNRK
SVKGNTALHDCAESGSLDIMKMLLMYCAKMEKDGYGMTPLLSASVTGHTNIVDFLTHHAQ
TSKTERINALELLGATFVDKKRDLLGALKYWKKAMNMRYSDRTNIISKPVPQTLIMAYDY
AKEVNSAEELEGLIADPDEMRMQALLIRERILGPSHPDTSYYIRYRGAVYADSGNFKRCI
NLWKYALDMQQSNLDPLSPMTASSLLSFAELFGGGSGGGSGGGSGGGSKKRLLLGLDR

Primary citation

Molecular basis for arginine C-terminal degron recognition by Cul2 FEM1 E3 ligase. Chen, X., Liao, S., Makaros, Y. et al. Nat Chem Biol (2021) 17:254-262. DOI 10.1038/s41589-020-00704-3 · PubMed

Other PDB entries of the same protein (UniProt Q15078 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3O0G 1.95 Å, Crystal Structure of Cdk5:p25 in complex with an ATP analogue
7VDP 2.09 Å, The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 1
1UNL 2.2 Å, Structural mechanism for the inhibition of CD5-p25 from the roscovitine, aloisine and…
1UNG 2.3 Å, Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and…
1UNH 2.35 Å, Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and…
7VDR 2.55 Å, The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 13
1H4L 2.65 Å, Structure and regulation of the CDK5-p25(nck5a) complex
7VDQ 2.91 Å, The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 7
7VDS 3.05 Å, The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 24
7CNG 3.49 Å, Structure of CDK5R1 bound FEM1B

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