MolNFT v1 · #113094 · protein

Crystal structure of the RPF2-RRS1 complex

5A53 · Regulator of ribosome biosynthesis: “Crystal structure of the RPF2-RRS1 complex”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.60). MolNFT v1 #113094 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5A53
Type: protein
Length: 312 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Regulator of ribosome biosynthesis; Ribosome biogenesis protein RPF2
UniProt: Q08746, P36160
Ligands: SO4
Pockets: 6 · best druggability 0.60

Structure

x-ray diffraction · 3 distinct chains · 26% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Regulator of ribosome biosynthesis	protein	65	42% helix, 15% strand	Q08746
B	Regulator of ribosome biosynthesis	protein	22	0% helix, 18% strand	Q08746
C	Ribosome biogenesis protein RPF2	protein	225	24% helix, 34% strand	P36160

Ligands and binding sites

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

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	240	0.60	0.80	32	SO4
2	103	0.46	0.79	18	empty
3	76	0.45	0.81	24	empty
4	94	0.36	0.75	18	empty
5	87	0.36	0.75	19	empty

Interfaces

3 interfaces between chains.

A–C · 1624 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 1117 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 550 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5A53 · Crystal Structure of the Rpf2-Rrs1 complex · the same entry in another collection · chain A against A, TM-score 1.00
P36160 · AlphaFold monomer V2.0 prediction for ribosome biogenesis protein RPF2 (P36160) · a predicted model of the same protein · chain C against A, TM-score 0.99
Q08746 · AlphaFold monomer V2.0 prediction for regulator of ribosome biosynthesis (Q08746) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 Q08746
Every structure of UniProt P36160
Elsewhere: RCSB PDB 5A53 · PDBe 5A53 · UniProt Q08746 · UniProt P36160

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