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Crystal structure of the chromatin-tethering domain of human cytomegalovirus IE1 protein bound to the nucleosome core particle

Analyse Crystal structure of the chromatin-tethering domain of human cytomegalovirus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5E5A
Type: protein + DNA
Length: 1,070 residues
Chains: 11
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (146-mer); Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; C-terminal domain…
UniProt: P84233, P62799, Q6AZJ8, P02281, Q6SWP6
Ligands: MG
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 9 distinct chains · 63% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
I, J	DNA (146-mer)	dna	146	—	—
A	Histone H3.2	protein	99	63% helix, 4% strand	P84233
B	Histone H4	protein	79	63% helix, 9% strand	P62799
C, G	Histone H2A	protein	105	56% helix, 7% strand	Q6AZJ8
D	Histone H2B 1.1	protein	98	71% helix, 4% strand	P02281
E	Histone H3.2	protein	98	67% helix, 4% strand	P84233
F	Histone H4	protein	86	58% helix, 8% strand	P62799
H	Histone H2B 1.1	protein	94	74% helix, 4% strand	P02281
K	C-terminal domain of regulatory protein IE1	protein	14	0% helix, 0% strand	Q6SWP6

Ligands and binding sites

MG · Magnesium ion · metal · 4 copies · chains I, J, C, D, E

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	1052	0.82	0.83	103	empty
2	465	0.78	0.86	59	empty
3	566	0.77	0.84	59	empty
4	796	0.71	0.77	81	empty
5	489	0.65	0.78	32	empty

Interfaces

38 interfaces between chains.

I–J · 6391 Å² buried · 566 hydrogen bonds · nucleic-nucleic
E–F · 2648 Å² buried · 24 hydrogen bonds · protein-protein
G–H · 2604 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 2604 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 2540 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

5E5A · Crystal structure of the chromatin-tethering domain of Human cytomegalovirus IE1 protein… · the same entry in another collection · chain I against I, 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 P84233
Every structure of UniProt P62799
Every structure of UniProt Q6AZJ8
Every structure of UniProt P02281
Every structure of UniProt Q6SWP6
Elsewhere: RCSB PDB 5E5A · PDBe 5E5A · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt Q6SWP6

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