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Crystal structure of S. pombe DCP1/DCP2 in complex with H. sapiens PNRC2 and synthetic cap analog

Analyse Crystal structure of S. pombe DCP1/DCP2 in complex with H. sapiens PNRC2 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KQ4
Type: protein
Length: 772 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MRNA-decapping enzyme subunit 1; Proline-rich nuclear receptor coactivator 2; MRNA…
EC: 3.-.-.-
UniProt: Q9P805, Q9NPJ4, O13828
Ligands: 6VQ
Pockets: 8 · best druggability 0.70

Structure

x-ray diffraction · 6 distinct chains · 35% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	MRNA-decapping enzyme subunit 1	protein	126	28% helix, 48% strand	Q9P805
F	Proline-rich nuclear receptor coactivator 2	protein	22	27% helix, 0% strand	Q9NPJ4
E	MRNA decapping complex subunit 2 (EC 3.-.-.-)	protein	235	37% helix, 20% strand	O13828
A	MRNA-decapping enzyme subunit 1	protein	124	26% helix, 48% strand	Q9P805
C	Proline-rich nuclear receptor coactivator 2	protein	23	26% helix, 0% strand	Q9NPJ4
B	MRNA decapping complex subunit 2 (EC 3.-.-.-)	protein	242	43% helix, 15% strand	O13828

Ligands and binding sites

6VQ · [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-3~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate · ligand · 2 copies · chains D, E, B

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

Pockets

8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	675	0.70	0.78	64	6VQ
2	655	0.67	0.76	71	empty
3	99	0.47	0.80	20	empty
4	79	0.40	0.79	21	empty
5	70	0.40	0.79	12	empty

Interfaces

9 interfaces between chains.

D–E · 1120 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1078 Å² buried · 17 hydrogen bonds · protein-protein
D–F · 840 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 826 Å² buried · 3 hydrogen bonds · protein-protein
F–A · 326 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5KQ4 · Crystal structure of S. pombe Dcp1/Dcp2 in complex with H. sapiens PNRC2 and synthetic… · the same entry in another collection · chain B against B, 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 D against A, TM-score 0.99
O13828 · AlphaFold monomer V2.0 prediction for mRNA decapping complex subunit 2 (O13828) · a predicted model of the same protein · chain B against A, TM-score 0.59
Q9NPJ4 · AlphaFold monomer V2.0 prediction for proline-rich nuclear receptor coactivator 2 (Q9NPJ4) · a predicted model of the same protein · chain F against A, TM-score 0.49

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 Q9NPJ4
Every structure of UniProt O13828
Elsewhere: RCSB PDB 5KQ4 · PDBe 5KQ4 · UniProt Q9P805 · UniProt Q9NPJ4 · UniProt O13828

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