MolNFT v1 · #142994 · protein

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

6AM0 · KLLA0F23980P: “Crystal structure of K. lactis EDC1-DCP1-DCP2-EDC3 decapping complex with synthetic cap substrate analog”. X-ray diffraction, 2 ligands (6VQ, MG), 13 pockets (best druggability 0.77). MolNFT v1 #142994 on GenesisL1…

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

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