MolNFT v1 · #119382 · protein

Crystal structure of a human YL1-H2A.Z-H2B complex

5FUG · Histone H2A.Z: “Crystal structure of a human YL1-H2A.Z-H2B complex”. X-ray diffraction, 6 pockets (best druggability 0.51). MolNFT v1 #119382 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5FUG
Type: protein
Length: 920 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H2A.Z; Histone H2B type 1-J; Vacuolar protein sorting-associated protein 72…
UniProt: P0C0S5, P06899, Q15906
Pockets: 6 · best druggability 0.51

Structure

x-ray diffraction · 11 distinct chains · 58% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone H2A.Z	protein	89	65% helix, 4% strand	P0C0S5
B	Histone H2B type 1-J	protein	90	76% helix, 6% strand	P06899
C	Vacuolar protein sorting-associated protein 72 homolog	protein	51	25% helix, 10% strand	Q15906
D	Histone H2A.Z	protein	84	69% helix, 4% strand	P0C0S5
E	Histone H2B type 1-J	protein	91	75% helix, 4% strand	P06899
F	Vacuolar protein sorting-associated protein 72 homolog	protein	59	19% helix, 8% strand	Q15906
G	Histone H2A.Z	protein	82	66% helix, 5% strand	P0C0S5
H, K	Histone H2B type 1-J	protein	89	78% helix, 6% strand	P06899
I	Vacuolar protein sorting-associated protein 72 homolog	protein	54	28% helix, 7% strand	Q15906
J	Histone H2A.Z	protein	85	62% helix, 5% strand	P0C0S5
L	Vacuolar protein sorting-associated protein 72 homolog	protein	57	26% helix, 7% strand	Q15906

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	79	0.51	0.84	24	empty
2	105	0.39	0.76	18	empty
3	57	0.30	0.76	16	empty
4	59	0.30	0.75	14	empty
5	63	0.28	0.73	16	empty

Interfaces

30 interfaces between chains.

A–B · 2745 Å² buried · 24 hydrogen bonds · protein-protein
J–K · 2672 Å² buried · 31 hydrogen bonds · protein-protein
D–E · 2605 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 2528 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 1425 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

5FUG · Crystal structure of a human YL1-H2A.Z-H2B complex · the same entry in another collection · chain L against L, 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 P0C0S5
Every structure of UniProt P06899
Every structure of UniProt Q15906
Elsewhere: RCSB PDB 5FUG · PDBe 5FUG · UniProt P0C0S5 · UniProt P06899 · UniProt Q15906

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