MolNFT v1 · #127097 · protein + RNA

Structure of the large subunit of the chloroplast ribosome

5MMI · 50S ribosomal protein L31: “Structure of the large subunit of the chloroplast ribosome”. Electron microscopy, 2 ligands (MG, ZN), 20 pockets (best druggability 0.90). MolNFT v1 #127097 on GenesisL1: 3D structure, binding sites and…

PDB: 5MMI
Type: protein + RNA
Length: 6,796 residues
Chains: 35
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 50S ribosomal protein L31; 50S ribosomal protein L32, chloroplastic; 50S ribosomal…
UniProt: A0A0K9R0R6, P28804, P28805, P82244, P23326, P12230, A0A0K9S2M7, P82411, P06509, A0A0K9QEC7, A0A0K9RVQ9, A0A0K9RJX4, A0A0K9R4N9, A0A0K9RQ91, A0A0K9R3N5, P31164, P12629, P09596, A0A0K9QHT0, P17353, A0A0K9RLJ4, A0A0K9QQ60, P82413, P28803, P24613, P09594, Q9LWB5, A0A0K9QFU9, A0A0K9R4I2, A0A0K9RD02, A0A0K9R7W8
Ligands: MG, ZN
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · 35 distinct chains · 30% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	50S ribosomal protein L31	protein	44	0% helix, 32% strand	A0A0K9R0R6
1	50S ribosomal protein L32, chloroplastic	protein	48	60% helix, 4% strand	P28804
2	50S ribosomal protein L33, chloroplastic	protein	60	0% helix, 42% strand	P28805
3	50S ribosomal protein L34, chloroplastic	protein	60	43% helix, 0% strand	P82244
4	50S ribosomal protein L35, chloroplastic	protein	72	28% helix, 10% strand	P23326
5	50S ribosomal protein L36, chloroplastic	protein	37	8% helix, 43% strand	P12230
6	Plastid ribosomal protein CL37, PSRP5	protein	49	84% helix, 0% strand	A0A0K9S2M7
7	50S ribosomal protein 6, chloroplastic	protein	46	24% helix, 9% strand	P82411
A	23S ribosomal RNA	rna	2798	—	—
B	5S ribosomal RNA	rna	121	—	—
C	50S ribosomal protein L2, chloroplastic	protein	253	7% helix, 27% strand	P06509
D	Plastid ribosomal protein UL3C	protein	221	10% helix, 33% strand	A0A0K9QEC7
E	Plastid ribosomal protein UL4C	protein	212	33% helix, 14% strand	A0A0K9RVQ9
F	Plastid ribosomal protein UL5C	protein	193	35% helix, 18% strand	A0A0K9RJX4
G	Plastid ribosomal protein UL6C	protein	178	22% helix, 38% strand	A0A0K9R4N9
H	Plastid ribosomal protein BL9C	protein	48	23% helix, 31% strand	A0A0K9RQ91
I	Plastid ribosomal protein UL10C	protein	137	51% helix, 19% strand	A0A0K9R3N5
J	50S ribosomal protein L11, chloroplastic	protein	133	41% helix, 16% strand	P31164
K	50S ribosomal protein L13, chloroplastic	protein	203	36% helix, 14% strand	P12629
L	50S ribosomal protein L14, chloroplastic	protein	121	7% helix, 42% strand	P09596
M	Plastid ribosomal protein UL15C	protein	185	27% helix, 10% strand	A0A0K9QHT0
N	50S ribosomal protein L16, chloroplastic	protein	135	20% helix, 28% strand	P17353
O	Plastid ribosomal protein BL17C	protein	116	52% helix, 15% strand	A0A0K9RLJ4
P	Plastid ribosomal protein UL18C	protein	122	40% helix, 24% strand	A0A0K9QQ60
Q	50S ribosomal protein L19, chloroplastic	protein	118	22% helix, 36% strand	P82413
R	50S ribosomal protein L20, chloroplastic	protein	119	74% helix, 0% strand	P28803
S	50S ribosomal protein L21, chloroplastic	protein	170	13% helix, 38% strand	P24613
T	50S ribosomal protein L22, chloroplastic	protein	172	46% helix, 24% strand	P09594
U	50S ribosomal protein L23, chloroplastic	protein	96	33% helix, 23% strand	Q9LWB5
V	Plastid ribosomal protein UL24C	protein	134	7% helix, 44% strand	A0A0K9QFU9
W	4.5S ribosomal RNA	rna	106	—	—
X	Plastid ribosomal protein BL27C	protein	109	19% helix, 27% strand	A0A0K9R4I2
Y	Plastid ribosomal protein BL28C	protein	77	23% helix, 34% strand	A0A0K9RD02
Z	Plastid ribosomal protein UL29C	protein	101	76% helix, 0% strand	A0A0K9R7W8
z	E-site tRNA	rna	2	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 501 copies · chains 4, A, 6, 7, C, E, 3, D, O, M, K, T, U, S, Q, Z, X, R, Y, N, V, B, W, H, P
ZN · Zinc ion · metal · 2 copies · chains 2, 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	884	0.90	0.93	112	MG
2	1097	0.87	0.89	86	MG
3	700	0.87	0.92	77	MG
4	843	0.87	0.90	91	MG
5	632	0.87	0.92	66	MG

Interfaces

77 interfaces between chains.

A–C · 6789 Å² buried · 160 hydrogen bonds · protein-nucleic
A–M · 5725 Å² buried · 130 hydrogen bonds · protein-nucleic
A–D · 4733 Å² buried · 85 hydrogen bonds · protein-nucleic
A–E · 4720 Å² buried · 103 hydrogen bonds · protein-nucleic
A–R · 4210 Å² buried · 108 hydrogen bonds · protein-nucleic

Compared structures

5MMI · Structure of the large subunit of the chloroplast ribosome · the same entry in another collection · chain C against C, 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 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 P82411
Every structure of UniProt P06509
Every structure of UniProt A0A0K9QEC7
Every structure of UniProt A0A0K9RVQ9
Every structure of UniProt A0A0K9RJX4
Every structure of UniProt A0A0K9R4N9
Every structure of UniProt A0A0K9RQ91
Every structure of UniProt A0A0K9R3N5
Every structure of UniProt P31164
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 A0A0K9QFU9
Every structure of UniProt A0A0K9R4I2
Every structure of UniProt A0A0K9RD02
Every structure of UniProt A0A0K9R7W8
Elsewhere: RCSB PDB 5MMI · PDBe 5MMI · UniProt A0A0K9R0R6 · UniProt P28804 · UniProt P28805 · UniProt P82244 · UniProt P23326 · UniProt P12230 · UniProt A0A0K9S2M7 · UniProt P82411 · UniProt P06509 · UniProt A0A0K9QEC7 · UniProt A0A0K9RVQ9 · UniProt A0A0K9RJX4 · UniProt A0A0K9R4N9 · UniProt A0A0K9RQ91 · UniProt A0A0K9R3N5 · UniProt P31164 · UniProt P12629 · UniProt P09596 · UniProt A0A0K9QHT0 · UniProt P17353 · UniProt A0A0K9RLJ4 · UniProt A0A0K9QQ60 · UniProt P82413 · UniProt P28803 · UniProt P24613 · UniProt P09594 · UniProt Q9LWB5 · UniProt A0A0K9QFU9 · UniProt A0A0K9R4I2 · UniProt A0A0K9RD02 · UniProt A0A0K9R7W8

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