MolNFT v1 · #119498 · protein

Structure of the human RBBP4:MTA1(464-546) complex

5FXY · Histone-binding protein RBBP4: “Structure of the human RBBP4:MTA1(464-546) complex”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #119498 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5FXY
Type: protein
Length: 1,796 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone-binding protein RBBP4; Metastasis-associated protein MTA1
UniProt: Q09028, Q13330
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 5 distinct chains · 19% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, G	Histone-binding protein RBBP4	protein	381	9% helix, 42% strand	Q09028
B, D	Metastasis-associated protein MTA1	protein	69	54% helix, 4% strand	Q13330
C, E	Histone-binding protein RBBP4	protein	380	9% helix, 42% strand	Q09028
F	Metastasis-associated protein MTA1	protein	68	54% helix, 6% strand	Q13330
H	Metastasis-associated protein MTA1	protein	68	54% helix, 4% strand	Q13330

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	296	0.83	0.94	32	empty
2	1129	0.82	0.83	81	empty
3	378	0.76	0.86	29	empty
4	376	0.76	0.86	33	empty
5	469	0.75	0.84	35	empty

Interfaces

16 interfaces between chains.

A–B · 2912 Å² buried · 39 hydrogen bonds · protein-protein
G–H · 2797 Å² buried · 39 hydrogen bonds · protein-protein
C–D · 2797 Å² buried · 36 hydrogen bonds · protein-protein
E–F · 2745 Å² buried · 31 hydrogen bonds · protein-protein
B–E · 322 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5FXY · Structure of the human RBBP4:MTA1(464-546) complex · the same entry in another collection · chain H against H, TM-score 1.00
Q09028 · AlphaFold monomer V2.0 prediction for histone-binding protein RBBP4 (Q09028) · a predicted model of the same protein · chain C against A, TM-score 0.98
Q13330 · AlphaFold monomer V2.0 prediction for metastasis-associated protein MTA1 (Q13330) · a predicted model of the same protein · chain F against A, TM-score 0.79

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 Q13330
Elsewhere: RCSB PDB 5FXY · PDBe 5FXY · UniProt Q09028 · UniProt Q13330

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