MolNFT v1 · #170917 · protein

Crystal structure of histone chaperone aplf acidic domain bound to the histone H2A-H2B-H3-H4 octamer

6YN1: “Crystal structure of histone chaperone aplf acidic domain bound to the histone H2A-H2B-H3-H4 octamer”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.82). MolNFT v1 #170917 on GenesisL1: 3D structure, binding…

PDB: 6YN1
Type: protein
Length: 3,071 residues
Chains: 40
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H2A; Histone H2B; Histone H3; Histone H4; Aprataxin and pnk-like factor
EC: 4.2.99.18
UniProt: Q6AZJ8, A0A1L8FQA5, A0A310TTQ1, P62799, Q8IW19
Ligands: CL
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 21 distinct chains · 61% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F, K	Histone H2A	protein	103	57% helix, 7% strand	Q6AZJ8
B	Histone H2B	protein	90	76% helix, 6% strand	A0A1L8FQA5
C, H, R, W, g, l	Histone H3	protein	94	72% helix, 4% strand	A0A310TTQ1
D, I	Histone H4	protein	76	61% helix, 9% strand	P62799
E, T, Y	Aprataxin and pnk-like factor (EC 4.2.99.18)	protein	22	0% helix, 9% strand	Q8IW19
G, L, Q, f, k	Histone H2B	protein	88	77% helix, 6% strand	A0A1L8FQA5
J	Aprataxin and pnk-like factor (EC 4.2.99.18)	protein	29	0% helix, 10% strand	Q8IW19
M	Histone H3	protein	95	72% helix, 4% strand	A0A310TTQ1
N, h	Histone H4	protein	75	61% helix, 9% strand	P62799
O, i	Aprataxin and pnk-like factor (EC 4.2.99.18)	protein	21	0% helix, 10% strand	Q8IW19
P	Histone H2A	protein	104	59% helix, 7% strand	Q6AZJ8
S	Histone H4	protein	77	60% helix, 9% strand	P62799
U, Z, j	Histone H2A	protein	103	58% helix, 7% strand	Q6AZJ8
V, a	Histone H2B	protein	89	76% helix, 6% strand	A0A1L8FQA5
X	Histone H4	protein	77	65% helix, 9% strand	P62799
b	Histone H3	protein	96	71% helix, 4% strand	A0A310TTQ1
c	Histone H4	protein	76	64% helix, 9% strand	P62799
d	Aprataxin and pnk-like factor (EC 4.2.99.18)	protein	20	0% helix, 10% strand	Q8IW19
e	Histone H2A	protein	102	59% helix, 7% strand	Q6AZJ8
m	Histone H4	protein	75	61% helix, 9% strand	P62799
n	Aprataxin and pnk-like factor (EC 4.2.99.18)	protein	20	0% helix, 10% strand	Q8IW19

Ligands and binding sites

CL · Chloride ion · ion · chains J
GOL · Glycerol · additive · 14 copies · chains A, H, I, C, D, K, R, S, M, N, P, U, b, c, e, l, m, g, h, j, k

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	818	0.82	0.85	71	empty
2	666	0.82	0.86	57	empty
3	1099	0.82	0.83	82	GOL
4	852	0.81	0.84	75	GOL
5	914	0.81	0.83	75	empty

Interfaces

158 interfaces between chains.

A–B · 2581 Å² buried · 30 hydrogen bonds · protein-protein
j–k · 2571 Å² buried · 26 hydrogen bonds · protein-protein
F–G · 2562 Å² buried · 23 hydrogen bonds · protein-protein
P–Q · 2531 Å² buried · 20 hydrogen bonds · protein-protein
U–V · 2523 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

6YN1 · Crystal structure of histone chaperone APLF acidic domain bound to the histone… · the same entry in another collection · chain J against J, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q6AZJ8
Every structure of UniProt A0A1L8FQA5
Every structure of UniProt A0A310TTQ1
Every structure of UniProt P62799
Every structure of UniProt Q8IW19
Elsewhere: RCSB PDB 6YN1 · PDBe 6YN1 · UniProt Q6AZJ8 · UniProt A0A1L8FQA5 · UniProt A0A310TTQ1 · UniProt P62799 · UniProt Q8IW19

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