MolNFT v1 · #187600 · protein

P107 pocket domain complexed with mutated HDAC1-3X peptide

7SMF · Retinoblastoma-like protein 1: “P107 pocket domain complexed with mutated HDAC1-3X peptide”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.74). MolNFT v1 #187600 on GenesisL1: 3D structure, binding sites and…

PDB: 7SMF
Type: protein
Length: 704 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinoblastoma-like protein 1; Histone deacetylase 1
EC: 3.5.1.98, 3.5.1.-
UniProt: P28749
Ligands: SO4
Pockets: 10 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 57% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Retinoblastoma-like protein 1	protein	342	59% helix, 1% strand	P28749
B, D	Histone deacetylase 1 (EC 3.5.1.98, 3.5.1.-)	protein	10	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, C

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

Pockets

10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	805	0.74	0.79	86	empty
2	200	0.52	0.78	24	empty
3	97	0.49	0.82	19	empty
4	116	0.42	0.76	18	empty
5	99	0.38	0.75	18	empty

Interfaces

3 interfaces between chains.

A–C · 1080 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 687 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 652 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

7SMF · p107 pocket domain complexed with mutated HDAC1-3X peptide · the same entry in another collection · chain A against A, TM-score 1.00
P28749 · AlphaFold monomer V2.0 prediction for retinoblastoma-like protein 1 (P28749) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P28749
Elsewhere: RCSB PDB 7SMF · PDBe 7SMF · UniProt P28749

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