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Crystal structure of K. lactis EDC1-DCP1-DCP2-EDC3 decapping complex with synthetic cap substrate analog

Analyse Crystal structure of K. lactis EDC1-DCP1-DCP2-EDC3 decapping complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AM0
Type: protein
Length: 1,042 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: KLLA0F23980P; KLLA0E01827P; KLLA0A01474P; KLLA0A11308P
UniProt: Q6CIU1, Q6CPV9, Q6CYC5, Q6CX48
Ligands: 6VQ, MG
Pockets: 13 · best druggability 0.77

Structure

x-ray diffraction · 8 distinct chains · 31% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	KLLA0F23980P	protein	260	45% helix, 17% strand	Q6CIU1
B	KLLA0E01827P	protein	175	23% helix, 36% strand	Q6CPV9
C	KLLA0A01474P	protein	23	13% helix, 0% strand	Q6CYC5
D	KLLA0A11308P	protein	65	5% helix, 54% strand	Q6CX48
E	KLLA0F23980P	protein	257	46% helix, 14% strand	Q6CIU1
F	KLLA0E01827P	protein	178	22% helix, 34% strand	Q6CPV9
G	KLLA0A01474P	protein	26	12% helix, 0% strand	Q6CYC5
H	KLLA0A11308P	protein	58	5% helix, 55% strand	Q6CX48

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 A, E
MG · Magnesium ion · metal · chains A

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

Pockets

13 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	886	0.77	0.80	84	6VQ
2	560	0.76	0.83	48	MG
3	586	0.74	0.81	63	empty
4	270	0.70	0.85	38	empty
5	165	0.67	0.86	17	empty

Interfaces

16 interfaces between chains.

E–F · 1779 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1676 Å² buried · 26 hydrogen bonds · protein-protein
F–G · 845 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 819 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 670 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6AM0 · Crystal structure of K. lactis Edc1-Dcp1-Dcp2-Edc3 decapping complex with synthetic cap… · the same entry in another collection · chain A against A, TM-score 1.00

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 Q6CIU1
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Every structure of UniProt Q6CX48
Elsewhere: RCSB PDB 6AM0 · PDBe 6AM0 · UniProt Q6CIU1 · UniProt Q6CPV9 · UniProt Q6CYC5 · UniProt Q6CX48

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