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Structure of the retinoblastoma protein pocket domain in complex with adenovirus E1A CR1 domain

Analyse Structure of the retinoblastoma protein pocket domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2R7G
Type: protein
Length: 702 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinoblastoma-associated protein; Early E1A 32 kda protein
UniProt: P06400, P03255
Ligands: SO4
Pockets: 11 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 70% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Retinoblastoma-associated protein	protein	336	71% helix, 1% strand	P06400
B, D	Early E1A 32 kda protein	protein	10	40% helix, 0% strand	P03255
C	Retinoblastoma-associated protein	protein	337	72% helix, 1% strand	P06400
E	Early E1A 32 kda protein	protein	9	0% helix, 0% strand	P03255

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, C

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

Pockets

11 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	1099	0.84	0.84	70	empty
2	201	0.51	0.77	29	empty
3	194	0.48	0.76	28	empty
4	89	0.39	0.77	16	empty
5	79	0.37	0.77	17	empty

Interfaces

4 interfaces between chains.

A–C · 1404 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 846 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 829 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 475 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

2R7G · Structure of the retinoblastoma protein pocket domain in complex with adenovirus E1A CR1… · the same entry in another collection · chain B against B, TM-score 1.00
P06400 · AlphaFold monomer V2.0 prediction for retinoblastoma-associated protein (P06400) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P06400
Every structure of UniProt P03255
Elsewhere: RCSB PDB 2R7G · PDBe 2R7G · UniProt P06400 · UniProt P03255

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