MolNFT v1 · #139216 · protein + RNA

Structure of the 50S large subunit of chloroplast ribosome from spinach

5X8T · 50S ribosomal protein L32, chloroplastic: “Structure of the 50S large subunit of chloroplast ribosome from spinach”. Electron microscopy, 20 pockets (best druggability 0.89). MolNFT v1 #139216 on GenesisL1: 3D structure, binding…

PDB: 5X8T
Type: protein + RNA
Length: 6,382 residues
Chains: 32
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 50S ribosomal protein L32, chloroplastic; 50S ribosomal protein L33, chloroplastic; 50S…
UniProt: P28804, P28805, P82244, P23326, P12230, A0A0K9S2M7, A0A0K9RCH6, P06509, A0A0K9QEC7, O49937, P82192, A0A0K9R4N9, A0A0K9RQ91, P12629, P09596, A0A0K9QHT0, P17353, A0A0K9RLJ4, A0A0K9QQ60, P82413, P28803, P24613, P09594, Q9LWB5, P27683, A0A0K9R4I2, A0A0K9RD02, A0A0K9R7W8, A0A0K9R0R6
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 32 distinct chains · 23% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	50S ribosomal protein L32, chloroplastic	protein	46	54% helix, 0% strand	P28804
2	50S ribosomal protein L33, chloroplastic	protein	51	0% helix, 22% strand	P28805
3	50S ribosomal protein L34, chloroplastic	protein	57	44% helix, 0% strand	P82244
4	50S ribosomal protein L35, chloroplastic	protein	69	20% helix, 14% strand	P23326
5	50S ribosomal protein L36, chloroplastic	protein	37	8% helix, 32% strand	P12230
6	Protein CL37	protein	49	80% helix, 0% strand	A0A0K9S2M7
7	Protein CL38	protein	46	9% helix, 4% strand	A0A0K9RCH6
B	5S rRNA	rna	117	—	—
C	50S ribosomal protein L2, chloroplastic	protein	247	3% helix, 21% strand	P06509
D	Protein L3	protein	212	8% helix, 37% strand	A0A0K9QEC7
E	50S ribosomal protein L4, chloroplastic	protein	210	27% helix, 6% strand	O49937
F	50S ribosomal protein L5, chloroplastic	protein	175	26% helix, 10% strand	P82192
G	Protein L6	protein	173	20% helix, 36% strand	A0A0K9R4N9
H	Protein L9	protein	53	23% helix, 15% strand	A0A0K9RQ91
K	50S ribosomal protein L13, chloroplastic	protein	193	28% helix, 11% strand	P12629
L	50S ribosomal protein L14, chloroplastic	protein	121	7% helix, 33% strand	P09596
M	Protein L15	protein	177	19% helix, 7% strand	A0A0K9QHT0
N	50S ribosomal protein L16, chloroplastic	protein	134	21% helix, 23% strand	P17353
O	Protein L17	protein	116	46% helix, 11% strand	A0A0K9RLJ4
P	Protein L18	protein	120	34% helix, 20% strand	A0A0K9QQ60
Q	50S ribosomal protein L19, chloroplastic	protein	118	18% helix, 31% strand	P82413
R	50S ribosomal protein L20, chloroplastic	protein	115	68% helix, 0% strand	P28803
S	50S ribosomal protein L21, chloroplastic	protein	147	3% helix, 38% strand	P24613
T	50S ribosomal protein L22, chloroplastic	protein	144	28% helix, 24% strand	P09594
U	50S ribosomal protein L23, chloroplastic	protein	92	24% helix, 27% strand	Q9LWB5
V	50S ribosomal protein L24, chloroplastic	protein	124	7% helix, 29% strand	P27683
W	4.8S rRNA	rna	102	—	—
X	Protein L27	protein	100	15% helix, 22% strand	A0A0K9R4I2
Y	Protein L28	protein	74	23% helix, 30% strand	A0A0K9RD02
Z	Protein L29	protein	90	69% helix, 0% strand	A0A0K9R7W8
A	23S rRNA	rna	2809	—	—
0	50S ribosomal protein L31	protein	64	13% helix, 28% strand	A0A0K9R0R6

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	746	0.89	0.94	109	empty
2	1194	0.88	0.90	135	empty
3	721	0.88	0.92	78	empty
4	762	0.87	0.91	77	empty
5	637	0.86	0.92	66	empty

Interfaces

71 interfaces between chains.

C–A · 6898 Å² buried · 144 hydrogen bonds · protein-nucleic
M–A · 5764 Å² buried · 128 hydrogen bonds · protein-nucleic
E–A · 4786 Å² buried · 90 hydrogen bonds · protein-nucleic
D–A · 4551 Å² buried · 90 hydrogen bonds · protein-nucleic
R–A · 4300 Å² buried · 77 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5X8T · Structure of the 50S large subunit of chloroplast ribosome from spinach · the same entry in another collection · chain 5 against 5, 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 P28804
Every structure of UniProt P28805
Every structure of UniProt P82244
Every structure of UniProt P23326
Every structure of UniProt P12230
Every structure of UniProt A0A0K9S2M7
Every structure of UniProt A0A0K9RCH6
Every structure of UniProt P06509
Every structure of UniProt A0A0K9QEC7
Every structure of UniProt O49937
Every structure of UniProt P82192
Every structure of UniProt A0A0K9R4N9
Every structure of UniProt A0A0K9RQ91
Every structure of UniProt P12629
Every structure of UniProt P09596
Every structure of UniProt A0A0K9QHT0
Every structure of UniProt P17353
Every structure of UniProt A0A0K9RLJ4
Every structure of UniProt A0A0K9QQ60
Every structure of UniProt P82413
Every structure of UniProt P28803
Every structure of UniProt P24613
Every structure of UniProt P09594
Every structure of UniProt Q9LWB5
Every structure of UniProt P27683
Every structure of UniProt A0A0K9R4I2
Every structure of UniProt A0A0K9RD02
Every structure of UniProt A0A0K9R7W8
Every structure of UniProt A0A0K9R0R6
Elsewhere: RCSB PDB 5X8T · PDBe 5X8T · UniProt P28804 · UniProt P28805 · UniProt P82244 · UniProt P23326 · UniProt P12230 · UniProt A0A0K9S2M7 · UniProt A0A0K9RCH6 · UniProt P06509 · UniProt A0A0K9QEC7 · UniProt O49937 · UniProt P82192 · UniProt A0A0K9R4N9 · UniProt A0A0K9RQ91 · UniProt P12629 · UniProt P09596 · UniProt A0A0K9QHT0 · UniProt P17353 · UniProt A0A0K9RLJ4 · UniProt A0A0K9QQ60 · UniProt P82413 · UniProt P28803 · UniProt P24613 · UniProt P09594 · UniProt Q9LWB5 · UniProt P27683 · UniProt A0A0K9R4I2 · UniProt A0A0K9RD02 · UniProt A0A0K9R7W8 · UniProt A0A0K9R0R6

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