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PCE1 guanylyltransferase bound to SPT5 ctd

Analyse PCE1 guanylyltransferase bound to SPT5 ctd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4PZ8
Type: protein
Length: 372 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MRNA-capping enzyme subunit alpha; Transcription elongation factor SPT5
EC: 2.7.7.50
UniProt: P40997
Ligands: SO4
Pockets: 3 · best druggability 0.44

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MRNA-capping enzyme subunit alpha (EC 2.7.7.50)	protein	368	27% helix, 32% strand	P40997
B	Transcription elongation factor SPT5	protein	4	0% helix, 25% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 11 copies · chains A

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	115	0.44	0.77	27	empty
2	113	0.43	0.77	23	SO4
3	77	0.41	0.79	15	empty

Interfaces

1 interface between chains.

A–B · 315 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (nonstandard).

Compared structures

4PZ8 · PCE1 guanylyltransferase bound to SPT5 CTD · the same entry in another collection · chain A against A, TM-score 1.00
P40997 · AlphaFold monomer V2.0 prediction for mRNA-capping enzyme subunit alpha (P40997) · a predicted model of the same protein · chain A 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 P40997
Elsewhere: RCSB PDB 4PZ8 · PDBe 4PZ8 · UniProt P40997

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