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The crystal structure of fission yeast mRNA decapping enzyme DCP1-DCP2 complex

Analyse The crystal structure of fission yeast mRNA decapping enzyme DCP1-DCP2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QKM
Type: protein
Length: 1,416 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SPBC3B9.21 protein; SPAC19A8.12 protein
EC: 3.6.1.30
UniProt: Q9P805, O13828
Ligands: ATP
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 7 distinct chains · 35% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	SPBC3B9.21 protein (EC 3.6.1.30)	protein	123	28% helix, 46% strand	Q9P805
B	SPAC19A8.12 protein	protein	266	42% helix, 19% strand	O13828
C	SPBC3B9.21 protein (EC 3.6.1.30)	protein	123	26% helix, 50% strand	Q9P805
D	SPAC19A8.12 protein	protein	202	35% helix, 13% strand	O13828
F	SPAC19A8.12 protein	protein	262	42% helix, 17% strand	O13828
G	SPBC3B9.21 protein (EC 3.6.1.30)	protein	127	24% helix, 44% strand	Q9P805
H	SPAC19A8.12 protein	protein	190	35% helix, 14% strand	O13828

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains B, F

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	880	0.79	0.81	101	empty
2	331	0.77	0.88	44	empty
3	121	0.76	0.95	21	empty
4	726	0.76	0.81	77	empty
5	296	0.76	0.89	45	empty

Interfaces

11 interfaces between chains.

B–D · 1364 Å² buried · 17 hydrogen bonds · protein-protein
F–H · 1350 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 1054 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1025 Å² buried · 17 hydrogen bonds · protein-protein
G–H · 910 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

2QKM · The crystal structure of fission yeast mRNA decapping enzyme Dcp1-Dcp2 complex · the same entry in another collection · chain H against H, TM-score 1.00
Q9P805 · AlphaFold monomer V2.0 prediction for mRNA-decapping enzyme subunit 1 (Q9P805) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 Q9P805
Every structure of UniProt O13828
Elsewhere: RCSB PDB 2QKM · PDBe 2QKM · UniProt Q9P805 · UniProt O13828

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