MolNFT v1 · #135204 · protein

Structure of mycobacterium tuberculosis proteasome in complex with N, C-capped dipeptide PKS2208

5TS0 · Proteasome subunit alpha: “Structure of mycobacterium tuberculosis proteasome in complex with N, C-capped dipeptide PKS2208”. X-ray diffraction, 1 ligand (7J1), 20 pockets (best druggability 0.83). MolNFT v1 #135204 on GenesisL1: 3D…

PDB: 5TS0
Type: protein
Length: 6,159 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: 7J1
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 11 distinct chains · 42% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, P	Proteasome subunit alpha (EC 3.4.25.1)	protein	218	43% helix, 25% strand	A5U4D5
B	Proteasome subunit alpha (EC 3.4.25.1)	protein	216	43% helix, 25% strand	A5U4D5
C	Proteasome subunit alpha (EC 3.4.25.1)	protein	217	43% helix, 25% strand	A5U4D5
D, R, U	Proteasome subunit alpha (EC 3.4.25.1)	protein	217	42% helix, 26% strand	A5U4D5
F	Proteasome subunit alpha (EC 3.4.25.1)	protein	215	42% helix, 26% strand	A5U4D5
G	Proteasome subunit alpha (EC 3.4.25.1)	protein	220	43% helix, 25% strand	A5U4D5
H, I, J, M, X, Z	Proteasome subunit beta (EC 3.4.25.1)	protein	222	41% helix, 29% strand	A5U4D6
K, L, N, V, W, Y, a, b	Proteasome subunit beta (EC 3.4.25.1)	protein	223	39% helix, 30% strand	A5U4D6
O	Proteasome subunit alpha (EC 3.4.25.1)	protein	216	42% helix, 26% strand	A5U4D5
Q, S	Proteasome subunit alpha (EC 3.4.25.1)	protein	218	42% helix, 25% strand	A5U4D5
T	Proteasome subunit alpha (EC 3.4.25.1)	protein	218	43% helix, 25% strand	A5U4D5

Ligands and binding sites

7J1 · (2S)-N-{(2S)-3-methoxy-1-[(naphthalen-1-ylmethyl) amino]-1-oxopropan-2-yl}-4-oxo-2-[(3-phenylpropanoyl) amino]-4-(1H-pyrrol-1-yl)butanamide (non-preferred name) · 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	553	0.83	0.89	44	empty
2	550	0.83	0.89	51	empty
3	602	0.82	0.87	44	empty
4	644	0.82	0.87	57	empty
5	530	0.82	0.88	48	empty

Interfaces

70 interfaces between chains.

P–Q · 969 Å² buried · 11 hydrogen bonds · protein-protein
R–S · 923 Å² buried · 13 hydrogen bonds · protein-protein
F–G · 904 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 898 Å² buried · 11 hydrogen bonds · protein-protein
A–G · 894 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

5TS0 · Structure of Mycobacterium tuberculosis proteasome in complex with N,C-capped dipeptide… · the same entry in another collection · chain I against I, 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 5TS0 · PDBe 5TS0 · UniProt A5U4D5 · UniProt A5U4D6

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