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Crystal structure of mycobacterium tuberculosis proteasome in complex with phenylimidazole-based inhibitor A85

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: 6OCW
Type: protein
Length: 6,137 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: M6M
Pockets: 20 · best druggability 0.86

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	43% helix, 25% strand	P9WHU1
B, Q	Proteasome subunit alpha (EC 3.4.25.1)	protein	215	40% helix, 26% strand	P9WHU1
C, U	Proteasome subunit alpha (EC 3.4.25.1)	protein	216	43% helix, 26% strand	P9WHU1
D	Proteasome subunit alpha (EC 3.4.25.1)	protein	215	42% helix, 26% strand	P9WHU1
E, P	Proteasome subunit alpha (EC 3.4.25.1)	protein	216	44% helix, 25% strand	P9WHU1
F	Proteasome subunit alpha (EC 3.4.25.1)	protein	214	40% helix, 26% strand	P9WHU1
G	Proteasome subunit alpha (EC 3.4.25.1)	protein	216	44% helix, 26% strand	P9WHU1
H, I, J, M, X, Z, b	Proteasome subunit beta (EC 3.4.25.1)	protein	222	41% helix, 29% strand	P9WHT9
K, L, N, V, W, Y, a	Proteasome subunit beta (EC 3.4.25.1)	protein	223	40% helix, 29% strand	P9WHT9
O	Proteasome subunit alpha (EC 3.4.25.1)	protein	215	43% helix, 26% strand	P9WHU1
R	Proteasome subunit alpha (EC 3.4.25.1)	protein	215	43% helix, 26% strand	P9WHU1
S	Proteasome subunit alpha (EC 3.4.25.1)	protein	218	44% helix, 25% strand	P9WHU1
T	Proteasome subunit alpha (EC 3.4.25.1)	protein	217	43% helix, 25% strand	P9WHU1

Ligands and binding sites

M6M · N-{(2S)-1-({(2S)-1-[(2,4-difluorobenzyl)amino]-1-oxopropan-2-yl}amino)-4-[(2S)-2-methylpiperidin-1-yl]-1,4-dioxobutan-2-yl}-5-methyl-1,2-oxazole-3-carboxamide (non-preferred name) · ligand · 14 copies · chains H, I, J, K, L, M, N, V, W, X, Y, Z, a, b
DMF · Dimethylformamide · additive · 15 copies · chains A, G, H, C, D, E, F, N, B, J, O, W, P, X, Q, Y, R, Z, S, T, U, a
CIT · Citric acid · additive · 14 copies · chains H, Y, I, X, J, W, K, V, L, b, M, a, N, 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	1170	0.86	0.87	109	M6M
2	597	0.84	0.89	48	empty
3	582	0.83	0.88	47	empty
4	581	0.83	0.88	48	empty
5	560	0.83	0.88	46	empty

Interfaces

70 interfaces between chains.

A–G · 950 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 924 Å² buried · 11 hydrogen bonds · protein-protein
T–U · 918 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 912 Å² buried · 12 hydrogen bonds · protein-protein
O–P · 909 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

P9WHT9 · AlphaFold monomer V2.0 prediction for proteasome subunit beta (P9WHT9) · a predicted model of the same protein · chain H against A, TM-score 1.00
P9WHU1 · AlphaFold monomer V2.0 prediction for proteasome subunit alpha (P9WHU1) · a predicted model of the same protein · chain G against A, TM-score 0.99

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 6OCW · PDBe 6OCW · UniProt P9WHU1 · UniProt P9WHT9

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