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Macrocyclic peptides TDI5575 that selectively inhibit the mycobacterium tuberculosis proteasome

Analyse Macrocyclic peptides TDI5575 that selectively inhibit the mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WNK
Type: protein
Length: 6,148 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: A5U4D5, A5U4D6
Ligands: U5Y
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 15 distinct chains · 42% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proteasome subunit alpha (EC 3.4.25.1)	protein	216	42% helix, 25% strand	A5U4D5
B	Proteasome subunit alpha (EC 3.4.25.1)	protein	215	43% helix, 26% strand	A5U4D5
C	Proteasome subunit alpha (EC 3.4.25.1)	protein	216	43% helix, 25% strand	A5U4D5
D, R	Proteasome subunit alpha (EC 3.4.25.1)	protein	217	43% helix, 26% strand	A5U4D5
E	Proteasome subunit alpha (EC 3.4.25.1)	protein	214	43% helix, 26% strand	A5U4D5
F	Proteasome subunit alpha (EC 3.4.25.1)	protein	216	42% helix, 25% strand	A5U4D5
G	Proteasome subunit alpha (EC 3.4.25.1)	protein	220	41% helix, 25% strand	A5U4D5
H, b	Proteasome subunit beta (EC 3.4.25.1)	protein	224	41% helix, 29% strand	A5U4D6
I, J, L, M, N, V, X, Z, a	Proteasome subunit beta (EC 3.4.25.1)	protein	222	40% helix, 29% strand	A5U4D6
K, W, Y	Proteasome subunit beta (EC 3.4.25.1)	protein	223	41% helix, 30% strand	A5U4D6
O	Proteasome subunit alpha (EC 3.4.25.1)	protein	215	43% helix, 26% strand	A5U4D5
P	Proteasome subunit alpha (EC 3.4.25.1)	protein	218	42% helix, 25% strand	A5U4D5
Q, S	Proteasome subunit alpha (EC 3.4.25.1)	protein	218	43% helix, 25% strand	A5U4D5
T	Proteasome subunit alpha (EC 3.4.25.1)	protein	215	42% helix, 24% strand	A5U4D5
U	Proteasome subunit alpha (EC 3.4.25.1)	protein	218	42% helix, 25% strand	A5U4D5

Ligands and binding sites

U5Y · (12S,15S)-N-[(2-fluorophenyl)methyl]-10,13-dioxo-12-{2-oxo-2-[(2R)-2-phenylpyrrolidin-1-yl]ethyl}-2-oxa-11, 14-diazatricyclo[15.2.2.1~3,7~]docosa-1(19),3(22),4,6, 17,20-hexaene-15-carboxamide · ligand · 14 copies · chains H, I, J, K, L, M, N, V, W, X, Y, Z, a, b
CIT · Citric acid · additive · 14 copies · chains H, I, X, J, K, V, L, b, M, a, N, Z, W, Y
DMF · Dimethylformamide · additive · 8 copies · chains O, P, Q, R, Y, S, V, W, X

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	1129	0.86	0.87	113	U5Y, CIT
2	548	0.84	0.90	45	empty
3	584	0.84	0.89	50	empty
4	548	0.84	0.90	47	empty
5	593	0.84	0.89	46	empty

Interfaces

70 interfaces between chains.

A–G · 924 Å² buried · 9 hydrogen bonds · protein-protein
Q–R · 888 Å² buried · 8 hydrogen bonds · protein-protein
P–Q · 882 Å² buried · 9 hydrogen bonds · protein-protein
S–T · 881 Å² buried · 13 hydrogen bonds · protein-protein
R–S · 874 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

A5U4D6 · AlphaFold monomer V2.0 prediction for proteasome subunit beta (A5U4D6) · a predicted model of the same protein · chain K 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 A5U4D5
Every structure of UniProt A5U4D6
Elsewhere: RCSB PDB 6WNK · PDBe 6WNK · UniProt A5U4D5 · UniProt A5U4D6

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