MolNFT v1 · #161689 · protein

Leishmania tarentolae proteasome 20S subunit complexed with GSK3494245

6QM7 · Proteasome ALPHA1 chain: “Leishmania tarentolae proteasome 20S subunit complexed with GSK3494245”. Electron microscopy, 1 ligand (J6E), 20 pockets (best druggability 0.83). MolNFT v1 #161689 on GenesisL1: 3D structure, binding sites…

PDB: 6QM7
Type: protein
Length: 6,350 residues
Chains: 28
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proteasome ALPHA1 chain; Proteasome ALPHA2 chain; Proteasome ALPHA3 chain; Proteasome…
Ligands: J6E
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 14 distinct chains · 34% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, O	Proteasome ALPHA1 chain	protein	244	39% helix, 26% strand	—
B, P	Proteasome ALPHA2 chain	protein	229	38% helix, 28% strand	—
C, Q	Proteasome ALPHA3 chain	protein	276	38% helix, 25% strand	—
D, R	Proteasome ALPHA4 chain	protein	239	38% helix, 24% strand	—
E, S	Proteasome ALPHA5 chain	protein	229	35% helix, 28% strand	—
F, T	Proteasome ALPHA6 chain	protein	238	34% helix, 27% strand	—
G, U	Proteasome ALPHA7 chain	protein	228	32% helix, 27% strand	—
H, V	Proteasome BETA1 chain	protein	229	31% helix, 28% strand	—
I, W	Proteasome BETA2 chain	protein	219	30% helix, 36% strand	—
J, X	Proteasome BETA3 chain	protein	204	30% helix, 34% strand	—
K, Y	Proteasome BETA4 chain	protein	206	32% helix, 33% strand	—
L, Z	Proteasome BETA5 chain	protein	202	35% helix, 33% strand	—
M, a	Proteasome BETA6 chain	protein	214	30% helix, 30% strand	—
N, b	Proteasome BETA7 chain	protein	218	36% helix, 30% strand	—

Ligands and binding sites

J6E · ~{N}-[4-fluoranyl-3-(3-morpholin-4-ylimidazo[1,2-a]pyrimidin-7-yl)phenyl]pyrrolidine-1-carboxamide · ligand · 2 copies · chains K, L, X, J, Y, Z

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1149	0.83	0.85	87	empty
2	1114	0.83	0.84	77	empty
3	445	0.81	0.89	44	empty
4	455	0.80	0.88	42	empty
5	960	0.79	0.81	115	empty

Interfaces

86 interfaces between chains.

H–b · 2417 Å² buried · 43 hydrogen bonds · protein-protein
N–V · 2409 Å² buried · 44 hydrogen bonds · protein-protein
I–J · 1749 Å² buried · 22 hydrogen bonds · protein-protein
W–X · 1742 Å² buried · 24 hydrogen bonds · protein-protein
P–Q · 1580 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

6QM7 · Leishmania tarentolae proteasome 20S subunit complexed with GSK3494245 · the same entry in another collection · chain B against B, 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
Elsewhere: RCSB PDB 6QM7 · PDBe 6QM7

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