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Complex of the large ribosomal subunit from deinococcus radiodurans with quinupristin and dalfopristin

Analyse Complex of the large ribosomal subunit from deinococcus radiodurans with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SM1
Type: protein + RNA
Length: 6,313 residues
Chains: 32
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S ribosomal RNA; 50S ribosomal protein L33; 50S ribosomal protein L34; 50S ribosomal…
UniProt: Q9RSS4, Q9RSH2, Q9RSW6, Q9RSK0, Q9RXJ9, Q9RXK2, Q9RXK1, Q9RXJ0, Q9RSL3, Q9RY49, Q9RSS7, Q9RXY1, Q9RXJ2, Q9RSK9, Q9RXJ5, Q9RSJ5, Q9RSL2, Q9RWB4, Q9RSW7, Q9RY64, Q9RXJ7, Q9RXK0, Q9RXJ1, Q9RX88, Q9RY65, Q9RXJ4, Q9RSL0, Q9RW44, P49228
Ligands: MHT, DOL
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 32 distinct chains · 0% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	23S ribosomal RNA	rna	2766	—	—
1	50S ribosomal protein L33	protein	53	0% helix, 0% strand	Q9RSS4
2	50S ribosomal protein L34	protein	46	0% helix, 0% strand	Q9RSH2
3	50S ribosomal protein L35	protein	63	0% helix, 0% strand	Q9RSW6
4	50S ribosomal protein L36	protein	35	0% helix, 0% strand	Q9RSK0
5	Quinupristin	protein	7	0% helix, 0% strand	—
9	5S ribosomal RNA	rna	118	—	—
A	50S ribosomal protein L2	protein	270	0% helix, 0% strand	Q9RXJ9
B	50S ribosomal protein L3	protein	205	0% helix, 0% strand	Q9RXK2
C	50S ribosomal protein L4	protein	197	0% helix, 0% strand	Q9RXK1
D	50S ribosomal protein L5	protein	178	0% helix, 0% strand	Q9RXJ0
E	50S ribosomal protein L6	protein	177	0% helix, 0% strand	Q9RSL3
F	50S ribosomal protein L9	protein	52	0% helix, 0% strand	Q9RY49
G	50S ribosomal protein L11	protein	143	0% helix, 0% strand	Q9RSS7
H	50S ribosomal protein L13	protein	143	0% helix, 0% strand	Q9RXY1
I	50S ribosomal protein L14	protein	132	0% helix, 0% strand	Q9RXJ2
J	50S ribosomal protein L15	protein	141	0% helix, 0% strand	Q9RSK9
K	50S ribosomal protein L16	protein	124	0% helix, 0% strand	Q9RXJ5
L	50S ribosomal protein L17	protein	114	0% helix, 0% strand	Q9RSJ5
M	50S ribosomal protein L18	protein	111	0% helix, 0% strand	Q9RSL2
N	50S ribosomal protein L19	protein	125	0% helix, 0% strand	Q9RWB4
O	50S ribosomal protein L20	protein	117	0% helix, 0% strand	Q9RSW7
P	50S ribosomal protein L21	protein	100	0% helix, 0% strand	Q9RY64
Q	50S ribosomal protein L22	protein	130	0% helix, 0% strand	Q9RXJ7
R	50S ribosomal protein L23	protein	93	0% helix, 0% strand	Q9RXK0
S	50S ribosomal protein L24	protein	113	0% helix, 0% strand	Q9RXJ1
T	General stress protein ctc	protein	223	0% helix, 0% strand	Q9RX88
U	50S ribosomal protein L27	protein	86	0% helix, 0% strand	Q9RY65
W	50S ribosomal protein L29	protein	65	0% helix, 0% strand	Q9RXJ4
X	50S ribosomal protein L30	protein	55	0% helix, 0% strand	Q9RSL0
Y	50S ribosomal protein L31	protein	73	0% helix, 0% strand	Q9RW44
Z	50S ribosomal protein L32	protein	58	0% helix, 0% strand	P49228

Ligands and binding sites

MHT · (3R)-3-(methylsulfanyl)-1-azabicyclo[2.2.2]octane · ligand · chains 0, 5
DOL · 5-(2-diethylamino-ethanesulfonyl)-21-hydroxy-10-isopropyl-11,19-dimethyl-9,26-dioxa-3,15,28-triaza-tricyclo[23.2.1.00,255]octacosa-1(27),12,17,19,25(28)-pentaene-2,8,14,23-tetraone · ligand · chains 0, 5

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	994	0.88	0.91	103	empty
2	894	0.88	0.91	92	empty
3	897	0.85	0.88	94	empty
4	936	0.85	0.87	83	empty
5	573	0.84	0.90	52	empty

Interfaces

53 interfaces between chains.

0–A · 3174 Å² buried · 0 hydrogen bonds · protein-nucleic
0–B · 2447 Å² buried · 0 hydrogen bonds · protein-nucleic
0–C · 1920 Å² buried · 0 hydrogen bonds · protein-nucleic
0–J · 1786 Å² buried · 0 hydrogen bonds · protein-nucleic
0–O · 1385 Å² buried · 0 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 5 modified, 1 covalent (nonstandard, covalent ligand).

Compared structures

1SM1 · Complex of the large ribosomal subunit from deinococcus radiodurans with quinupristin and… · the same entry in another collection · chain T against T, 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 Q9RSS4
Every structure of UniProt Q9RSH2
Every structure of UniProt Q9RSW6
Every structure of UniProt Q9RSK0
Every structure of UniProt Q9RXJ9
Every structure of UniProt Q9RXK2
Every structure of UniProt Q9RXK1
Every structure of UniProt Q9RXJ0
Every structure of UniProt Q9RSL3
Every structure of UniProt Q9RY49
Every structure of UniProt Q9RSS7
Every structure of UniProt Q9RXY1
Every structure of UniProt Q9RXJ2
Every structure of UniProt Q9RSK9
Every structure of UniProt Q9RXJ5
Every structure of UniProt Q9RSJ5
Every structure of UniProt Q9RSL2
Every structure of UniProt Q9RWB4
Every structure of UniProt Q9RSW7
Every structure of UniProt Q9RY64
Every structure of UniProt Q9RXJ7
Every structure of UniProt Q9RXK0
Every structure of UniProt Q9RXJ1
Every structure of UniProt Q9RX88
Every structure of UniProt Q9RY65
Every structure of UniProt Q9RXJ4
Every structure of UniProt Q9RSL0
Every structure of UniProt Q9RW44
Every structure of UniProt P49228
Elsewhere: RCSB PDB 1SM1 · PDBe 1SM1 · UniProt Q9RSS4 · UniProt Q9RSH2 · UniProt Q9RSW6 · UniProt Q9RSK0 · UniProt Q9RXJ9 · UniProt Q9RXK2 · UniProt Q9RXK1 · UniProt Q9RXJ0 · UniProt Q9RSL3 · UniProt Q9RY49 · UniProt Q9RSS7 · UniProt Q9RXY1 · UniProt Q9RXJ2 · UniProt Q9RSK9 · UniProt Q9RXJ5 · UniProt Q9RSJ5 · UniProt Q9RSL2 · UniProt Q9RWB4 · UniProt Q9RSW7 · UniProt Q9RY64 · UniProt Q9RXJ7 · UniProt Q9RXK0 · UniProt Q9RXJ1 · UniProt Q9RX88 · UniProt Q9RY65 · UniProt Q9RXJ4 · UniProt Q9RSL0 · UniProt Q9RW44 · UniProt P49228

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