Research workbench

Pseudomonas aeruginosa 50S ribosome from a clinical isolate

Analyse Pseudomonas aeruginosa 50S ribosome from a clinical isolate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6SPD
Type: protein + RNA
Length: 6,425 residues
Chains: 32
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S ribosomal RNA; 5S ribosomal RNA; 50S ribosomal protein L2; 50S ribosomal protein L3…
UniProt: A0A241XHA2, A0A072ZBZ2, A0A241XH26, A0A072ZMU2, A0A2V3F3S9, A0A072ZKF0, A0A2V3GYK0, A0A071L356, E2RXT6, A0A2V3D5Z8, A0A069QEB6, A0A072ZCA1, E2RXU0, A0A263PZC6, A0A069QEE3, A0A072ZDZ0, A0A1C7BCP0, E2RXT1, E2RXT7, A0A072ZBM5, A0A071LFT4, A0A072ZIQ9, E2RXU1, A0A072ZJG4, A0A069QB25, A0A140SG33, A0A087L9L7, A0A069QC44, E2RXU2
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 32 distinct chains · 20% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	23S ribosomal RNA	rna	2851	—	—
B	5S ribosomal RNA	rna	116	—	—
C	50S ribosomal protein L2	protein	271	3% helix, 24% strand	A0A241XHA2
D	50S ribosomal protein L3	protein	207	9% helix, 32% strand	A0A072ZBZ2
E	50S ribosomal protein L4	protein	199	26% helix, 8% strand	A0A241XH26
F	50S ribosomal protein L5	protein	175	23% helix, 10% strand	A0A072ZMU2
G	50S ribosomal protein L6	protein	173	17% helix, 27% strand	A0A2V3F3S9
H	50S ribosomal protein L9	protein	147	20% helix, 13% strand	A0A072ZKF0
I	50S ribosomal protein L11	protein	140	21% helix, 5% strand	A0A2V3GYK0
J	50S ribosomal protein L13	protein	141	28% helix, 13% strand	A0A071L356
K	50S ribosomal protein L14	protein	120	0% helix, 32% strand	E2RXT6
L	50S ribosomal protein L15	protein	143	18% helix, 13% strand	A0A2V3D5Z8
M	50S ribosomal protein L16	protein	135	17% helix, 26% strand	A0A069QEB6
N	50S ribosomal protein L17	protein	118	39% helix, 19% strand	A0A072ZCA1
O	50S ribosomal protein L18	protein	115	40% helix, 19% strand	E2RXU0
P	50S ribosomal protein L19	protein	113	6% helix, 35% strand	A0A263PZC6
Q	50S ribosomal protein L20	protein	117	67% helix, 0% strand	A0A069QEE3
R	50S ribosomal protein L21	protein	103	0% helix, 61% strand	A0A072ZDZ0
S	50S ribosomal protein L22	protein	109	35% helix, 33% strand	A0A1C7BCP0
T	50S ribosomal protein L23	protein	92	14% helix, 38% strand	E2RXT1
U	50S ribosomal protein L24	protein	103	0% helix, 41% strand	E2RXT7
V	50S ribosomal protein L25	protein	188	15% helix, 30% strand	A0A072ZBM5
W	50S ribosomal protein L27	protein	76	4% helix, 21% strand	A0A071LFT4
X	50S ribosomal protein L28	protein	77	23% helix, 23% strand	A0A072ZIQ9
Y	Ribosomal protein UL29	protein	60	73% helix, 0% strand	—
Z	50S ribosomal protein L30	protein	57	26% helix, 21% strand	E2RXU1
1	50S ribosomal protein L31	protein	31	13% helix, 0% strand	A0A072ZJG4
2	50S ribosomal protein L32	protein	53	15% helix, 15% strand	A0A069QB25
3	50S ribosomal protein L33	protein	50	0% helix, 46% strand	A0A140SG33
4	50S ribosomal protein L34	protein	44	52% helix, 0% strand	A0A087L9L7
5	50S ribosomal protein L35	protein	63	29% helix, 17% strand	A0A069QC44
6	50S ribosomal protein L36	protein	38	8% helix, 34% strand	E2RXU2

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	926	0.88	0.90	86	empty
2	940	0.87	0.89	92	empty
3	694	0.86	0.91	71	empty
4	591	0.85	0.91	69	empty
5	730	0.84	0.88	58	empty

Interfaces

62 interfaces between chains.

A–C · 6923 Å² buried · 117 hydrogen bonds · protein-nucleic
A–D · 4936 Å² buried · 76 hydrogen bonds · protein-nucleic
A–L · 4344 Å² buried · 71 hydrogen bonds · protein-nucleic
A–E · 4146 Å² buried · 60 hydrogen bonds · protein-nucleic
A–Q · 4085 Å² buried · 58 hydrogen bonds · protein-nucleic

Compared structures

6SPD · Pseudomonas aeruginosa 50s ribosome from a clinical isolate · the same entry in another collection · chain B against B, 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 A0A241XHA2
Every structure of UniProt A0A072ZBZ2
Every structure of UniProt A0A241XH26
Every structure of UniProt A0A072ZMU2
Every structure of UniProt A0A2V3F3S9
Every structure of UniProt A0A072ZKF0
Every structure of UniProt A0A2V3GYK0
Every structure of UniProt A0A071L356
Every structure of UniProt E2RXT6
Every structure of UniProt A0A2V3D5Z8
Every structure of UniProt A0A069QEB6
Every structure of UniProt A0A072ZCA1
Every structure of UniProt E2RXU0
Every structure of UniProt A0A263PZC6
Every structure of UniProt A0A069QEE3
Every structure of UniProt A0A072ZDZ0
Every structure of UniProt A0A1C7BCP0
Every structure of UniProt E2RXT1
Every structure of UniProt E2RXT7
Every structure of UniProt A0A072ZBM5
Every structure of UniProt A0A071LFT4
Every structure of UniProt A0A072ZIQ9
Every structure of UniProt E2RXU1
Every structure of UniProt A0A072ZJG4
Every structure of UniProt A0A069QB25
Every structure of UniProt A0A140SG33
Every structure of UniProt A0A087L9L7
Every structure of UniProt A0A069QC44
Every structure of UniProt E2RXU2
Elsewhere: RCSB PDB 6SPD · PDBe 6SPD · UniProt A0A241XHA2 · UniProt A0A072ZBZ2 · UniProt A0A241XH26 · UniProt A0A072ZMU2 · UniProt A0A2V3F3S9 · UniProt A0A072ZKF0 · UniProt A0A2V3GYK0 · UniProt A0A071L356 · UniProt E2RXT6 · UniProt A0A2V3D5Z8 · UniProt A0A069QEB6 · UniProt A0A072ZCA1 · UniProt E2RXU0 · UniProt A0A263PZC6 · UniProt A0A069QEE3 · UniProt A0A072ZDZ0 · UniProt A0A1C7BCP0 · UniProt E2RXT1 · UniProt E2RXT7 · UniProt A0A072ZBM5 · UniProt A0A071LFT4 · UniProt A0A072ZIQ9 · UniProt E2RXU1 · UniProt A0A072ZJG4 · UniProt A0A069QB25 · UniProt A0A140SG33 · UniProt A0A087L9L7 · UniProt A0A069QC44 · UniProt E2RXU2

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