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Structure of the RBBP5 beta-propeller domain

Analyse Structure of the RBBP5 beta-propeller domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OV3
Type: protein
Length: 653 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinoblastoma-binding protein 5
UniProt: Q8BX09
Pockets: 9 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 3% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Retinoblastoma-binding protein 5	protein	330	2% helix, 48% strand	Q8BX09
B	Retinoblastoma-binding protein 5	protein	317	3% helix, 50% strand	Q8BX09
C	Retinoblastoma-binding protein 5	protein	6	0% helix, 50% strand	Q8BX09

Ligands and binding sites

PGE · Triethylene glycol · additive · chains A
PG4 · Tetraethylene glycol · additive · chains A, B, C

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

Pockets

9 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	769	0.80	0.84	60	empty
2	679	0.80	0.84	58	empty
3	71	0.49	0.84	18	PG4
4	144	0.44	0.76	27	empty
5	91	0.42	0.78	20	PGE

Interfaces

3 interfaces between chains.

A–B · 1873 Å² buried · 50 hydrogen bonds · protein-protein
B–C · 326 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 78 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5OV3 · Structure of the RbBP5 beta-propeller domain · the same entry in another collection · chain A against A, TM-score 1.00
Q8BX09 · AlphaFold monomer V2.0 prediction for retinoblastoma-binding protein 5 (Q8BX09) · a predicted model of the same protein · chain B 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 Q8BX09
Elsewhere: RCSB PDB 5OV3 · PDBe 5OV3 · UniProt Q8BX09

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