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Crystal structure of mycobacterium tuberculosis proteasome at 2.2 a

Analyse Crystal structure of mycobacterium tuberculosis proteasome at 2.2 a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3MI0
Type: protein
Length: 6,168 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: O33244, O33245
Ligands: SA6
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 14 distinct chains · 42% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Proteasome subunit alpha (EC 3.4.25.1)	protein	215	42% helix, 26% strand	O33244
B	Proteasome subunit alpha (EC 3.4.25.1)	protein	213	41% helix, 26% strand	O33244
C, G, H, J, N, P	Proteasome subunit beta (EC 3.4.25.1)	protein	222	42% helix, 29% strand	O33245
D	Proteasome subunit alpha (EC 3.4.25.1)	protein	214	43% helix, 24% strand	O33244
E, L, T, X, Z, 2	Proteasome subunit beta (EC 3.4.25.1)	protein	223	41% helix, 29% strand	O33245
F	Proteasome subunit alpha (EC 3.4.25.1)	protein	220	41% helix, 25% strand	O33244
I	Proteasome subunit alpha (EC 3.4.25.1)	protein	216	43% helix, 25% strand	O33244
K, M, O, Y	Proteasome subunit alpha (EC 3.4.25.1)	protein	216	43% helix, 25% strand	O33244
Q	Proteasome subunit alpha (EC 3.4.25.1)	protein	215	43% helix, 26% strand	O33244
R, V	Proteasome subunit beta (EC 3.4.25.1)	protein	239	42% helix, 28% strand	O33245
S	Proteasome subunit alpha (EC 3.4.25.1)	protein	216	42% helix, 25% strand	O33244
U	Proteasome subunit alpha (EC 3.4.25.1)	protein	216	42% helix, 25% strand	O33244
W	Proteasome subunit alpha (EC 3.4.25.1)	protein	216	41% helix, 26% strand	O33244
1	Proteasome subunit alpha (EC 3.4.25.1)	protein	215	42% helix, 26% strand	O33244

Ligands and binding sites

SA6 · (2R,3S,4R)-2-[(S)-(1S)-cyclohex-2-en-1-yl(hydroxy)methyl]-4-ethyl-3-hydroxy-3-methyl-5-oxopyrrolidine-2-carbaldehyde · ligand · 14 copies · chains C, E, G, V, H, L, J, R, N, P, T, Z, X, 2
DMF · Dimethylformamide · additive · 123 copies · chains A, H, B, C, I, J, E, R, D, Q, K, L, F, G, N, V, 2, X, P, T, M, O, Y, Z, S, U, W, 1

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	1110	0.87	0.89	104	DMF, SA6
2	1050	0.86	0.87	98	DMF, SA6
3	1068	0.86	0.87	102	DMF, SA6
4	580	0.85	0.90	48	DMF
5	597	0.85	0.90	47	DMF

Interfaces

71 interfaces between chains.

F–W · 1147 Å² buried · 19 hydrogen bonds · protein-protein
J–R · 1095 Å² buried · 21 hydrogen bonds · protein-protein
G–V · 1088 Å² buried · 21 hydrogen bonds · protein-protein
B–I · 962 Å² buried · 11 hydrogen bonds · protein-protein
Q–Y · 956 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 covalent (covalent ligand).

Compared structures

3MI0 · Crystal Structure of Mycobacterium Tuberculosis Proteasome at 2.2 A · the same entry in another collection · chain T against T, TM-score 1.00

Analyse

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Every structure of UniProt O33244
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Elsewhere: RCSB PDB 3MI0 · PDBe 3MI0 · UniProt O33244 · UniProt O33245

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