MolNFT v1 · #161690 · protein

Leishmania tarentolae proteasome 20S subunit apo structure

6QM8 · Proteasome ALPHA1 chain: “Leishmania tarentolae proteasome 20S subunit apo structure”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #161690 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6QM8
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…
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 14 distinct chains · 33% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, O	Proteasome ALPHA1 chain	protein	244	38% helix, 22% strand	—
B, P	Proteasome ALPHA2 chain	protein	229	36% helix, 25% strand	—
C, Q	Proteasome ALPHA3 chain	protein	276	36% helix, 22% strand	—
D, R	Proteasome ALPHA4 chain	protein	239	36% helix, 25% strand	—
E, S	Proteasome ALPHA5 chain	protein	229	31% helix, 27% strand	—
F, T	Proteasome ALPHA6 chain	protein	238	35% helix, 26% strand	—
G, U	Proteasome ALPHA7 chain	protein	228	31% helix, 26% strand	—
H, V	Proteasome BETA1 chain	protein	229	30% helix, 28% strand	—
I, W	Proteasome BETA2 chain	protein	219	30% helix, 33% strand	—
J, X	Proteasome BETA3 chain	protein	204	30% helix, 31% strand	—
K, Y	Proteasome BETA4 chain	protein	206	32% helix, 31% strand	—
L, Z	Proteasome BETA5 chain	protein	202	35% helix, 33% strand	—
M, a	Proteasome BETA6 chain	protein	214	30% helix, 25% strand	—
N, b	Proteasome BETA7 chain	protein	218	34% helix, 28% strand	—

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	1150	0.83	0.84	80	empty
2	1190	0.82	0.84	86	empty
3	422	0.80	0.88	41	empty
4	790	0.79	0.82	70	empty
5	1170	0.79	0.80	139	empty

Interfaces

86 interfaces between chains.

H–b · 2419 Å² buried · 34 hydrogen bonds · protein-protein
N–V · 2418 Å² buried · 36 hydrogen bonds · protein-protein
I–J · 1749 Å² buried · 21 hydrogen bonds · protein-protein
W–X · 1745 Å² buried · 22 hydrogen bonds · protein-protein
P–Q · 1556 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

6QM8 · Leishmania tarentolae proteasome 20S subunit apo structure · 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 6QM8 · PDBe 6QM8

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