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Structure of mycobacterium tuberculosis proteasome in complex with N, C-capped dipeptide PKS2206

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

PDB: 5TRY
Type: protein
Length: 6,152 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: 7J0
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 12 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	42% helix, 26% strand	A5U4D5
B	Proteasome subunit alpha (EC 3.4.25.1)	protein	215	43% helix, 26% strand	A5U4D5
C, T, U	Proteasome subunit alpha (EC 3.4.25.1)	protein	216	43% helix, 25% strand	A5U4D5
D	Proteasome subunit alpha (EC 3.4.25.1)	protein	217	43% helix, 26% strand	A5U4D5
E, R	Proteasome subunit alpha (EC 3.4.25.1)	protein	217	42% helix, 25% strand	A5U4D5
F	Proteasome subunit alpha (EC 3.4.25.1)	protein	218	40% helix, 25% strand	A5U4D5
G, O	Proteasome subunit alpha (EC 3.4.25.1)	protein	216	42% helix, 25% strand	A5U4D5
H, I, J, M, X, Z	Proteasome subunit beta (EC 3.4.25.1)	protein	222	40% helix, 30% strand	A5U4D6
K, L, N, V, W, Y, a, b	Proteasome subunit beta (EC 3.4.25.1)	protein	223	40% helix, 30% strand	A5U4D6
P	Proteasome subunit alpha (EC 3.4.25.1)	protein	217	41% helix, 26% strand	A5U4D5
Q	Proteasome subunit alpha (EC 3.4.25.1)	protein	218	44% helix, 25% strand	A5U4D5
S	Proteasome subunit alpha (EC 3.4.25.1)	protein	219	41% helix, 26% strand	A5U4D5

Ligands and binding sites

7J0 · (2~{S})-~{N}-[(2~{S})-3-methoxy-1-(naphthalen-1-ylmethylamino)-1-oxidanylidene-propan-2-yl]-4-oxidanylidene-2-(3-phenylpropanoylamino)-4-piperidin-1-yl-butanamide · 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	1192	0.85	0.86	110	7J0
2	714	0.85	0.89	64	empty
3	541	0.84	0.90	48	empty
4	558	0.84	0.89	47	empty
5	544	0.83	0.89	48	empty

Interfaces

70 interfaces between chains.

A–B · 939 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 932 Å² buried · 13 hydrogen bonds · protein-protein
O–U · 904 Å² buried · 14 hydrogen bonds · protein-protein
T–U · 895 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 895 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

5TRY · Structure of Mycobacterium tuberculosis proteasome in complex with N,C-capped dipeptide… · 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 A5U4D5
Every structure of UniProt A5U4D6
Elsewhere: RCSB PDB 5TRY · PDBe 5TRY · UniProt A5U4D5 · UniProt A5U4D6

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