MolNFT v1 · #99502 · protein

Crystal structure of the UTP22 and RRP7 complex from saccharomyces cerevisiae

4M5D · U3 small nucleolar RNA-associated protein 22: “Crystal structure of the UTP22 and RRP7 complex from saccharomyces cerevisiae”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.84). MolNFT v1 #99502 on GenesisL1: 3D…

PDB: 4M5D
Type: protein
Length: 1,267 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: U3 small nucleolar RNA-associated protein 22; Ribosomal RNA-processing protein 7
UniProt: P53254, P25368
Ligands: SO4
Pockets: 14 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	U3 small nucleolar RNA-associated protein 22	protein	1098	44% helix, 16% strand	P53254
B	Ribosomal RNA-processing protein 7	protein	169	36% helix, 19% strand	P25368

Ligands and binding sites

SO4 · Sulfate ion · ion · 11 copies · chains A
PGE · Triethylene glycol · additive · 3 copies · chains A, B

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

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1049	0.84	0.85	89	empty
2	670	0.75	0.81	72	SO4
3	617	0.73	0.80	62	empty
4	357	0.70	0.82	45	empty
5	85	0.61	0.88	13	empty

Interfaces

1 interface between chains.

A–B · 3177 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

4M5D · Crystal structure of the Utp22 and Rrp7 complex from Saccharomyces cerevisiae · the same entry in another collection · chain A against A, TM-score 1.00
P53254 · AlphaFold monomer V2.0 prediction for U3 small nucleolar RNA- associated protein 22… · a predicted model of the same protein · chain A against A, TM-score 0.97
P25368 · AlphaFold monomer V2.0 prediction for ribosomal RNA-processing protein 7 (P25368) · a predicted model of the same protein · chain B against A, TM-score 0.92

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 P53254
Every structure of UniProt P25368
Elsewhere: RCSB PDB 4M5D · PDBe 4M5D · UniProt P53254 · UniProt P25368

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