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Structural basis for RBAP48 binding to fog-1

Analyse Structural basis for RBAP48 binding to fog-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2XU7
Type: protein
Length: 752 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone-binding protein RBBP4; Zinc finger protein ZFPM1
UniProt: Q09028, Q8IX07
Pockets: 9 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histone-binding protein RBBP4	protein	360	7% helix, 47% strand	Q09028
B	Histone-binding protein RBBP4	protein	367	8% helix, 46% strand	Q09028
C	Zinc finger protein ZFPM1	protein	12	0% helix, 0% strand	Q8IX07
D	Zinc finger protein ZFPM1	protein	13	0% helix, 0% strand	Q8IX07

Ligands and binding sites

PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	607	0.74	0.81	47	empty
2	410	0.73	0.84	33	empty
3	133	0.52	0.81	28	empty
4	88	0.52	0.84	17	empty
5	56	0.47	0.85	14	empty

Interfaces

4 interfaces between chains.

A–B · 919 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 807 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 795 Å² buried · 18 hydrogen bonds · protein-protein
B–D · 171 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2XU7 · Structural basis for RbAp48 binding to FOG-1 · the same entry in another collection · chain D against D, TM-score 1.00
Q09028 · AlphaFold monomer V2.0 prediction for histone-binding protein RBBP4 (Q09028) · a predicted model of the same protein · chain B against A, TM-score 0.99
Q8IX07 · AlphaFold monomer V2.0 prediction for zinc finger protein ZFPM1 (Q8IX07) · a predicted model of the same protein · chain C against A, TM-score 0.32

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 Q09028
Every structure of UniProt Q8IX07
Elsewhere: RCSB PDB 2XU7 · PDBe 2XU7 · UniProt Q09028 · UniProt Q8IX07

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