MolNFT v1 · #127098 · protein + RNA

Structure of the small subunit of the chloroplast ribosome

5MMJ · 50S ribosomal protein L31: “Structure of the small subunit of the chloroplast ribosome”. Electron microscopy, 1 ligand (MG), 20 pockets (best druggability 0.88). MolNFT v1 #127098 on GenesisL1: 3D structure, binding sites and…

PDB: 5MMJ
Type: protein + RNA
Length: 4,464 residues
Chains: 27
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 50S ribosomal protein L31; Plastid ribosomal protein BS1C; 16S ribosomal RNA; 30S…
UniProt: A0A0K9R0R6, P08242, P09595, P13788, Q9ST69, A0A0K9R0H2, P82129, P09597, A0A0K9RY17, A0A0K9RWE7, P06506, P62128, A0A0K9R024, P06507, Q9M3I4, P28807, A0A0K9RRR0, Q9M3K7, P06508, A0A0K9RHF9, P82277, P82412, P47910, P19954
Ligands: MG
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 27 distinct chains · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	50S ribosomal protein L31	protein	11	64% helix, 0% strand	A0A0K9R0R6
8	Plastid ribosomal protein BS1C	protein	174	34% helix, 21% strand	—
a	16S ribosomal RNA	rna	1484	—	—
b	30S ribosomal protein S2, chloroplastic	protein	233	50% helix, 14% strand	P08242
c	30S ribosomal protein S3, chloroplastic	protein	216	33% helix, 28% strand	P09595
d	30S ribosomal protein S4, chloroplastic	protein	199	44% helix, 9% strand	P13788
e	30S ribosomal protein S5, chloroplastic	protein	187	35% helix, 32% strand	Q9ST69
f	Plastid ribosomal protein BS6C	protein	113	24% helix, 37% strand	A0A0K9R0H2
g	30S ribosomal protein S7, chloroplastic	protein	154	56% helix, 8% strand	P82129
h	30S ribosomal protein S8, chloroplastic	protein	133	30% helix, 32% strand	P09597
i	Plastid ribosomal protein US9C	protein	144	35% helix, 19% strand	A0A0K9RY17
j	Plastid ribosomal protein US10C	protein	99	25% helix, 45% strand	A0A0K9RWE7
k	30S ribosomal protein S11, chloroplastic	protein	117	26% helix, 31% strand	P06506
l	30S ribosomal protein S12, chloroplastic	protein	122	9% helix, 28% strand	P62128
m	Plastid ribosomal protein US13C	protein	110	55% helix, 2% strand	A0A0K9R024
n	30S ribosomal protein S14, chloroplastic	protein	99	57% helix, 7% strand	P06507
o	30S ribosomal protein S15, chloroplastic	protein	75	73% helix, 0% strand	Q9M3I4
p	30S ribosomal protein S16, chloroplastic	protein	80	28% helix, 38% strand	P28807
q	Plastid ribosomal protein US17C	protein	86	3% helix, 45% strand	A0A0K9RRR0
r	30S ribosomal protein S18, chloroplastic	protein	60	43% helix, 5% strand	Q9M3K7
s	30S ribosomal protein S19 alpha, chloroplastic	protein	78	23% helix, 19% strand	P06508
t	Plastid ribosomal protein BS20C	protein	107	80% helix, 0% strand	—
u	Plastid ribosomal protein BS21C	protein	65	66% helix, 8% strand	A0A0K9RHF9
v	30S ribosomal protein 2, chloroplastic	protein	80	21% helix, 38% strand	P82277
w	30S ribosomal protein 3, chloroplastic	protein	82	38% helix, 29% strand	P82412
x	30S ribosomal protein S31, chloroplastic	protein	40	18% helix, 0% strand	P47910
y	Ribosome-binding factor PSRP1, chloroplastic	protein	116	36% helix, 29% strand	P19954

Ligands and binding sites

MG · Magnesium ion · metal · 185 copies · chains a, i, n, s, x, e, d, t, c, m, k, l

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	1045	0.88	0.90	105	MG
2	898	0.85	0.88	74	MG
3	1160	0.85	0.87	108	MG
4	700	0.83	0.88	64	MG
5	453	0.83	0.91	50	empty

Interfaces

56 interfaces between chains.

a–i · 3183 Å² buried · 89 hydrogen bonds · protein-nucleic
a–d · 3170 Å² buried · 70 hydrogen bonds · protein-nucleic
a–l · 3051 Å² buried · 62 hydrogen bonds · protein-nucleic
a–t · 2651 Å² buried · 56 hydrogen bonds · protein-nucleic
a–n · 2478 Å² buried · 60 hydrogen bonds · protein-nucleic

Compared structures

5MMJ · Structure of the small subunit of the chloroplast ribosome · 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 A0A0K9R0R6
Every structure of UniProt P08242
Every structure of UniProt P09595
Every structure of UniProt P13788
Every structure of UniProt Q9ST69
Every structure of UniProt A0A0K9R0H2
Every structure of UniProt P82129
Every structure of UniProt P09597
Every structure of UniProt A0A0K9RY17
Every structure of UniProt A0A0K9RWE7
Every structure of UniProt P06506
Every structure of UniProt P62128
Every structure of UniProt A0A0K9R024
Every structure of UniProt P06507
Every structure of UniProt Q9M3I4
Every structure of UniProt P28807
Every structure of UniProt A0A0K9RRR0
Every structure of UniProt Q9M3K7
Every structure of UniProt P06508
Every structure of UniProt A0A0K9RHF9
Every structure of UniProt P82277
Every structure of UniProt P82412
Every structure of UniProt P47910
Every structure of UniProt P19954
Elsewhere: RCSB PDB 5MMJ · PDBe 5MMJ · UniProt A0A0K9R0R6 · UniProt P08242 · UniProt P09595 · UniProt P13788 · UniProt Q9ST69 · UniProt A0A0K9R0H2 · UniProt P82129 · UniProt P09597 · UniProt A0A0K9RY17 · UniProt A0A0K9RWE7 · UniProt P06506 · UniProt P62128 · UniProt A0A0K9R024 · UniProt P06507 · UniProt Q9M3I4 · UniProt P28807 · UniProt A0A0K9RRR0 · UniProt Q9M3K7 · UniProt P06508 · UniProt A0A0K9RHF9 · UniProt P82277 · UniProt P82412 · UniProt P47910 · UniProt P19954

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