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Crystal structure of mycobacterium tuberculosis proteasome in complex with phenylimidazole-based inhibitor B6

Analyse Crystal structure of mycobacterium tuberculosis proteasome in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ODE
Type: protein
Length: 6,143 residues
Chains: 28
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Proteasome subunit alpha; Proteasome subunit beta
EC: 3.4.25.1
UniProt: P9WHU1, P9WHT9
Ligands: M9G
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 13 distinct chains · 42% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proteasome subunit alpha (EC 3.4.25.1)	protein	218	41% helix, 26% strand	P9WHU1
B, Q	Proteasome subunit alpha (EC 3.4.25.1)	protein	215	41% helix, 26% strand	P9WHU1
C, U	Proteasome subunit alpha (EC 3.4.25.1)	protein	216	43% helix, 25% strand	P9WHU1
D	Proteasome subunit alpha (EC 3.4.25.1)	protein	214	40% helix, 26% strand	P9WHU1
E, T	Proteasome subunit alpha (EC 3.4.25.1)	protein	217	42% helix, 26% strand	P9WHU1
F	Proteasome subunit alpha (EC 3.4.25.1)	protein	214	41% helix, 26% strand	P9WHU1
G	Proteasome subunit alpha (EC 3.4.25.1)	protein	216	43% helix, 25% strand	P9WHU1
H, I, J, M, X	Proteasome subunit beta (EC 3.4.25.1)	protein	222	40% helix, 29% strand	P9WHT9
K, L, N, V, W, Y, Z, a, b	Proteasome subunit beta (EC 3.4.25.1)	protein	223	39% helix, 30% strand	P9WHT9
O	Proteasome subunit alpha (EC 3.4.25.1)	protein	216	43% helix, 25% strand	P9WHU1
P	Proteasome subunit alpha (EC 3.4.25.1)	protein	219	42% helix, 25% strand	P9WHU1
R	Proteasome subunit alpha (EC 3.4.25.1)	protein	215	42% helix, 26% strand	P9WHU1
S	Proteasome subunit alpha (EC 3.4.25.1)	protein	218	43% helix, 25% strand	P9WHU1

Ligands and binding sites

M9G · N-{(2S)-1-({(1S)-1-[5-(2-fluorophenyl)-1H-imidazol-2-yl]ethyl}amino)-1,4-dioxo-4-[(2R)-2-phenylpyrrolidin-1-yl]butan-2-yl}-5-methyl-1,2-oxazole-3-carboxamide · ligand · 14 copies · chains H, I, J, K, L, M, N, V, W, X, Y, Z, a, b

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	1062	0.85	0.86	96	M9G
2	1152	0.85	0.86	108	M9G
3	1122	0.85	0.86	94	M9G
4	1165	0.85	0.86	115	M9G
5	572	0.83	0.89	45	empty

Interfaces

70 interfaces between chains.

O–U · 930 Å² buried · 15 hydrogen bonds · protein-protein
O–P · 912 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 907 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 893 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 892 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6ODE · Crystal Structure of Mycobacterium tuberculosis Proteasome in Complex with… · the same entry in another collection · chain K against K, 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 P9WHU1
Every structure of UniProt P9WHT9
Elsewhere: RCSB PDB 6ODE · PDBe 6ODE · UniProt P9WHU1 · UniProt P9WHT9

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