MolNFT v1 · #127074 · protein + DNA

Crystal structure of the pfv gag cbs bound to a mononucleosome

5MLU · Histone H3.2: “Crystal structure of the pfv gag cbs bound to a mononucleosome”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.81). MolNFT v1 #127074 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5MLU
Type: protein + DNA
Length: 1,057 residues
Chains: 11
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone H3.2; Histone H4; Histone H2A type 1; Histone H2B; Pfv gag peptide; DNA (145-mer)
UniProt: P84233, P62799, P06897, A0A1B8Y853
Ligands: MN
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 10 distinct chains · 63% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Histone H3.2	protein	97	67% helix, 4% strand	P84233
B	Histone H4	protein	84	58% helix, 8% strand	P62799
C	Histone H2A type 1	protein	103	56% helix, 7% strand	P06897
D	Histone H2B	protein	93	75% helix, 4% strand	A0A1B8Y853
F	Histone H4	protein	78	63% helix, 9% strand	P62799
G	Histone H2A type 1	protein	105	56% helix, 7% strand	P06897
H	Histone H2B	protein	94	74% helix, 4% strand	A0A1B8Y853
M	Pfv gag peptide	protein	16	0% helix, 0% strand	—
I	DNA (145-mer)	dna	145	—	—
J	DNA (145-mer)	dna	145	—	—

Ligands and binding sites

MN · Manganese (II) ion · metal · 4 copies · chains A, I, J

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	872	0.81	0.83	89	empty
2	398	0.81	0.90	41	empty
3	356	0.76	0.87	38	empty
4	639	0.72	0.80	58	empty
5	757	0.71	0.78	68	empty

Interfaces

40 interfaces between chains.

I–J · 6539 Å² buried · 549 hydrogen bonds · nucleic-nucleic
A–B · 2703 Å² buried · 22 hydrogen bonds · protein-protein
G–H · 2643 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 2579 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 2542 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

5MLU · Crystal structure of the PFV GAG CBS bound to a mononucleosome · the same entry in another collection · chain J against J, TM-score 1.00
P06897 · AlphaFold monomer V2.0 prediction for histone H2A type 1 (P06897) · a predicted model of the same protein · chain C against A, TM-score 0.96

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 P06897
Every structure of UniProt A0A1B8Y853
Elsewhere: RCSB PDB 5MLU · PDBe 5MLU · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt A0A1B8Y853

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