MolNFT v1 · #15567 · protein + RNA

Structure of large ribosomal subunit in complex with virginiamycin M

1N8R · 23S ribosomal RNA: “Structure of large ribosomal subunit in complex with virginiamycin M”. X-ray diffraction, 6 ligands (VIR, MG, NA), 20 pockets (best druggability 0.90). MolNFT v1 #15567 on GenesisL1: 3D structure, binding sites…

PDB: 1N8R
Type: protein + RNA
Length: 6,577 residues
Chains: 30
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S ribosomal RNA; 5S ribosomal RNA; 50S ribosomal protein L2P; 50S ribosomal protein…
UniProt: P20276, P20279, P12735, P14124, P14135, P12743, P15825, P29198, P22450, P12737, P14123, P12733, P14119, P12734, P10970, P12732, P10972, P14116, P10971, P14121, P18138, P12736, P32410, P22452, P32411
Ligands: VIR, MG, NA, CD, K, CL
Pockets: 20 · best druggability 0.90

Structure

x-ray diffraction · 30 distinct chains · 29% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	23S ribosomal RNA	rna	2754	—	—
B	5S ribosomal RNA	rna	122	—	—
C	50S ribosomal protein L2P	protein	237	13% helix, 24% strand	P20276
D	50S ribosomal protein L3P	protein	337	13% helix, 32% strand	P20279
E	50S ribosomal protein L4E	protein	246	34% helix, 15% strand	P12735
F	50S ribosomal protein L5P	protein	140	26% helix, 21% strand	P14124
G	50S ribosomal protein L6P	protein	172	22% helix, 42% strand	P14135
H	50S ribosomal protein L7AE	protein	119	48% helix, 13% strand	P12743
I	Acidic ribosomal protein P0 homolog	protein	29	79% helix, 0% strand	P15825
J	50S ribosomal protein L10E	protein	156	15% helix, 28% strand	—
K	50S ribosomal protein L13P	protein	142	40% helix, 15% strand	P29198
L	50S ribosomal protein L14P	protein	132	5% helix, 39% strand	P22450
M	50S ribosomal protein L15P	protein	145	19% helix, 16% strand	P12737
N	50S ribosomal protein L15E	protein	194	33% helix, 16% strand	—
O	50S ribosomal protein L18P	protein	186	40% helix, 13% strand	P14123
P	50S ribosomal protein L18E	protein	115	46% helix, 23% strand	P12733
Q	50S ribosomal protein L19E	protein	143	62% helix, 4% strand	P14119
R	50S ribosomal protein L21E	protein	95	14% helix, 32% strand	P12734
S	50S ribosomal protein L22P	protein	150	29% helix, 31% strand	P10970
T	50S ribosomal protein L23P	protein	81	35% helix, 31% strand	P12732
U	50S ribosomal protein L24P	protein	119	29% helix, 29% strand	P10972
V	50S ribosomal protein L24E	protein	53	19% helix, 19% strand	P14116
W	50S ribosomal protein L29P	protein	65	74% helix, 0% strand	P10971
X	50S ribosomal protein L30P	protein	154	38% helix, 14% strand	P14121
Y	50S ribosomal protein L31E	protein	82	39% helix, 28% strand	P18138
Z	50S ribosomal protein L32E	protein	142	23% helix, 12% strand	P12736
1	50S ribosomal protein L37AE	protein	73	36% helix, 18% strand	—
2	50S ribosomal protein L37E	protein	56	11% helix, 16% strand	P32410
3	50S ribosomal protein L39E	protein	46	39% helix, 0% strand	P22452
4	50S ribosomal protein L44E	protein	92	14% helix, 33% strand	P32411

Ligands and binding sites

VIR · Virginiamycin M1 · ligand · chains A
MG · Magnesium ion · metal · 117 copies · chains A, C, E, D, T, S, X, B, 3, 2, Z, 4, Q, N, 1, L, U
NA · Sodium ion · metal · 86 copies · chains A, M, D, 3, Z, S, B, K, E, N, F, C, J, R, T, U, 4
CD · Cadmium ion · metal · 5 copies · chains P, V, 1, 2, 4
K · Potassium ion · metal · chains A, N
CL · Chloride ion · ion · 22 copies · chains A, 3, R, M, K, X, C, D, G, L, N, F, O, P, S, Z, 4

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	1066	0.90	0.92	98	MG, NA
2	923	0.88	0.91	115	MG, CL
3	1055	0.87	0.89	96	MG, K, NA
4	688	0.86	0.91	85	empty
5	870	0.86	0.89	87	NA

Interfaces

53 interfaces between chains.

A–D · 7374 Å² buried · 224 hydrogen bonds · protein-nucleic
A–N · 6857 Å² buried · 174 hydrogen bonds · protein-nucleic
A–C · 6250 Å² buried · 177 hydrogen bonds · protein-nucleic
A–E · 5607 Å² buried · 131 hydrogen bonds · protein-nucleic
A–Q · 4360 Å² buried · 130 hydrogen bonds · protein-nucleic

Compared structures

1N8R · Structure of large ribosomal subunit in complex with virginiamycin M · the same entry in another collection · chain H against H, 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 P20276
Every structure of UniProt P20279
Every structure of UniProt P12735
Every structure of UniProt P14124
Every structure of UniProt P14135
Every structure of UniProt P12743
Every structure of UniProt P15825
Every structure of UniProt P29198
Every structure of UniProt P22450
Every structure of UniProt P12737
Every structure of UniProt P14123
Every structure of UniProt P12733
Every structure of UniProt P14119
Every structure of UniProt P12734
Every structure of UniProt P10970
Every structure of UniProt P12732
Every structure of UniProt P10972
Every structure of UniProt P14116
Every structure of UniProt P10971
Every structure of UniProt P14121
Every structure of UniProt P18138
Every structure of UniProt P12736
Every structure of UniProt P32410
Every structure of UniProt P22452
Every structure of UniProt P32411
Elsewhere: RCSB PDB 1N8R · PDBe 1N8R · UniProt P20276 · UniProt P20279 · UniProt P12735 · UniProt P14124 · UniProt P14135 · UniProt P12743 · UniProt P15825 · UniProt P29198 · UniProt P22450 · UniProt P12737 · UniProt P14123 · UniProt P12733 · UniProt P14119 · UniProt P12734 · UniProt P10970 · UniProt P12732 · UniProt P10972 · UniProt P14116 · UniProt P10971 · UniProt P14121 · UniProt P18138 · UniProt P12736 · UniProt P32410 · UniProt P22452 · UniProt P32411

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