4DO0: Human PHF8

Crystal Structure of human PHF8 in complex with Daminozide. Determined by X-ray diffraction at 2.55 Å resolution. Released 14 Mar 2012.

Method: X-ray diffraction
Resolution: 2.55 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,985
Mol. weight: 44.51 kDa
Ligands: ZN, DZA
Released: 14 Mar 2012

Explore 4DO0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4DO0 contains 19 α-helices and 16 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: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	85-93	9
β-strand	97-98	2	1
β-strand	104	1	2
α-helix	108-110	3
α-helix	113-119	7
β-strand	125-127	3	2
β-strand	136	1	3
α-helix	144-151	8
β-strand	156-161	6	2
β-strand	166-171	6	2
α-helix	172-181	10
β-strand	188-194	7	2
α-helix	199-203	5
β-strand	205	1	3
α-helix	208-213	6
α-helix	215-219	5
α-helix	227-229	3
β-strand	234-238	5	2
β-strand	242-247	6	1
α-helix	250-252	3
β-strand	254-261	8	2
β-strand	263-269	7	1
α-helix	273-284	12
α-helix	288-290	3
α-helix	293-295	3
β-strand	301-306	6	1
β-strand	310-313	4	2
β-strand	318-323	6	1
β-strand	327-334	8	2
α-helix	340-353	14
α-helix	364-384	21
α-helix	391-407	17
α-helix	413-416	4
α-helix	417-419	3
α-helix	426-439	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone lysine demethylase PHF8	A	protein	374	Homo sapiens	Q9UPP1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4DO0_1 Histone lysine demethylase PHF8 (chains A)
YFQSMPVKTGSPTFVRELRSRTFDSSDEVILKPTGNQLTVEFLEENSFSVPILVLKKDGL
GMTLPSPSFTVRDVEHYVGSDKEIDVIDVTRQADCKMKLGDFVKYYYSGKREKVLNVISL
EFSDTRLSNLVETPKIVRKLSWVENLWPEECVFERPNVQKYCLMSVRDSYTDFHIDFGGT
SVWYHVLKGEKIFYLIRPTNANLTLFECWSSSSNQNEMFFGDQVDKCYKCSVKQGQTLFI
PTGWIHAVLTPVDCLAFGGNFLHSLNIEMQLKAYEIEKRLSTADLFRFPNFETICWYVGK
HILDIFRGLRENRRHPASYLVHGGKALNLAFRAWTRKEALPDHEDEIPETVRTVQLIKDL
AREIRLVEDIFQQN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
DZA	Daminozide	C6 H12 N2 O3	1

Water and common crystallization additives (SO4, EDO, ACT) are not listed.

Other PDB entries of the same protein (UniProt Q9UPP1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7CMZ 1.7 Å, Crystal Structure of BRCT7/8 in Complex with the APS Motif of PHF8
3K3O 2.1 Å, Crystal structure of the catalytic core domain of human PHF8 complexed with…
2WWU 2.15 Å, Crystal structure of the catalytic domain of PHD finger protein 8
3KV4 2.19 Å, Structure of PHF8 in complex with histone H3
3K3N 2.4 Å, Crystal structure of the catalytic core domain of human PHF8

Browse structure collections

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