MolNFT v1 · #22034 · protein

Structure of dcps bound to M7GPPPA

1ST4 · MRNA decapping enzyme: “Structure of dcps bound to M7GPPPA”. X-ray diffraction, 2 ligands (GTA, YT3), 5 pockets (best druggability 0.85). MolNFT v1 #22034 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1ST4
Type: protein
Length: 597 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MRNA decapping enzyme
UniProt: Q96C86
Ligands: GTA, YT3
Pockets: 5 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	MRNA decapping enzyme	protein	297	32% helix, 30% strand	Q96C86
A	MRNA decapping enzyme	protein	300	30% helix, 30% strand	Q96C86

Ligands and binding sites

GTA · P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate · ligand · 2 copies · chains B, A
YT3 · Yttrium (III) ion · metal · 3 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1078	0.85	0.86	105	GTA
2	204	0.79	0.93	28	empty
3	200	0.54	0.78	28	empty
4	162	0.48	0.77	26	empty
5	91	0.43	0.79	16	GTA

Interfaces

1 interface between chains.

B–A · 4850 Å² buried · 79 hydrogen bonds · protein-protein

Compared structures

1ST4 · Structure of DcpS bound to m7GpppA · the same entry in another collection · chain B against B, TM-score 1.00
Q96C86 · AlphaFold monomer V2.0 prediction for M7GPPPX diphosphatase (Q96C86) · a predicted model of the same protein · chain A against A, TM-score 0.79

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 Q96C86
Elsewhere: RCSB PDB 1ST4 · PDBe 1ST4 · UniProt Q96C86

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