MolNFT v1 · #173214 · protein + RNA

Staphylococcus aureus 50S after 30 minutes incubation at 37C

7ASM · 50S ribosomal protein L19: “Staphylococcus aureus 50S after 30 minutes incubation at 37C”. Electron microscopy, 1 ligand (MG), 20 pockets (best druggability 0.90). MolNFT v1 #173214 on GenesisL1: 3D structure, binding sites and…

PDB: 7ASM
Type: protein + RNA
Length: 5,985 residues
Chains: 29
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 50S ribosomal protein L19; 50S ribosomal protein L4; 23S rRNA; 5S rRNA; 50S ribosomal…
UniProt: A0A077UVB6, W8TRC7, B3VKN3, W8U3X2, W8TUE6, A0A077UGA7, A0A077V4G0, W8TRE0, A0A077VMP6, D7URR3, W8TUB4, A0A6K7SSC4, A0A133Q8Z9, A0A077ULC5, A0A077W1J5, A0A077UL47, A0A077V2P0, W8TQ59, A0A077UGV8, W8U3W0, A0A2S6D0C0, A0A077UUA0, A0A6I4H7Y4, A0A077URJ8, W8UVN7, A0A1Q8DAT0, A0A077UG91
Ligands: MG
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · 29 distinct chains · 23% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
N	50S ribosomal protein L19	protein	114	18% helix, 39% strand	A0A077UVB6
E	50S ribosomal protein L4	protein	206	30% helix, 16% strand	W8TRC7
A	23S rRNA	rna	2834	—	—
B	5S rRNA	rna	115	—	—
C	50S ribosomal protein L2	protein	274	9% helix, 27% strand	B3VKN3
G	50S ribosomal protein L6	protein	175	22% helix, 33% strand	W8U3X2
H	50S ribosomal protein L13	protein	145	26% helix, 10% strand	W8TUE6
J	50S ribosomal protein L15	protein	146	16% helix, 9% strand	A0A077UGA7
K	50S ribosomal protein L16	protein	137	18% helix, 27% strand	A0A077V4G0
M	50S ribosomal protein L18	protein	119	33% helix, 19% strand	W8TRE0
O	50S ribosomal protein L20	protein	116	76% helix, 0% strand	A0A077VMP6
P	50S ribosomal protein L21	protein	102	0% helix, 58% strand	D7URR3
R	50S ribosomal protein L23	protein	89	27% helix, 40% strand	W8TUB4
S	50S ribosomal protein L24	protein	100	3% helix, 43% strand	A0A6K7SSC4
T	50S ribosomal protein L25	protein	94	21% helix, 49% strand	A0A133Q8Z9
U	50S ribosomal protein L27	protein	79	0% helix, 37% strand	A0A077ULC5
W	50S ribosomal protein L29	protein	67	76% helix, 0% strand	A0A077W1J5
3	50S ribosomal protein L35	protein	64	34% helix, 13% strand	A0A077UL47
1	50S ribosomal protein L33	protein	47	0% helix, 53% strand	A0A077V2P0
2	50S ribosomal protein L34	protein	43	58% helix, 0% strand	W8TQ59
4	50S ribosomal protein L36	protein	37	8% helix, 32% strand	A0A077UGV8
D	50S ribosomal protein L3	protein	215	6% helix, 33% strand	W8U3W0
F	50S ribosomal protein L5	protein	158	26% helix, 13% strand	A0A2S6D0C0
I	50S ribosomal protein L14	protein	122	7% helix, 29% strand	A0A077UUA0
Q	50S ribosomal protein L22	protein	112	34% helix, 35% strand	A0A6I4H7Y4
V	50S ribosomal protein L28	protein	49	12% helix, 49% strand	A0A077URJ8
X	50S ribosomal protein L30	protein	58	33% helix, 24% strand	W8UVN7
Z	50S ribosomal protein L32	protein	48	15% helix, 13% strand	A0A1Q8DAT0
L	50S ribosomal protein L17	protein	120	50% helix, 22% strand	A0A077UG91

Ligands and binding sites

MG · Magnesium ion · metal · chains A

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	1136	0.90	0.93	134	empty
2	970	0.86	0.89	75	empty
3	820	0.85	0.88	84	empty
4	670	0.85	0.89	69	empty
5	798	0.85	0.88	68	empty

Interfaces

54 interfaces between chains.

A–C · 6936 Å² buried · 134 hydrogen bonds · protein-nucleic
A–D · 5023 Å² buried · 104 hydrogen bonds · protein-nucleic
A–J · 4406 Å² buried · 91 hydrogen bonds · protein-nucleic
E–A · 4262 Å² buried · 72 hydrogen bonds · protein-nucleic
A–O · 3973 Å² buried · 87 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 5 disulfide, 3 modified (disulfide, nucleotide modification).

Compared structures

7ASM · Staphylococcus aureus 50S after 30 minutes incubation at 37C · the same entry in another collection · chain J against J, 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 A0A077UVB6
Every structure of UniProt W8TRC7
Every structure of UniProt B3VKN3
Every structure of UniProt W8U3X2
Every structure of UniProt W8TUE6
Every structure of UniProt A0A077UGA7
Every structure of UniProt A0A077V4G0
Every structure of UniProt W8TRE0
Every structure of UniProt A0A077VMP6
Every structure of UniProt D7URR3
Every structure of UniProt W8TUB4
Every structure of UniProt A0A6K7SSC4
Every structure of UniProt A0A133Q8Z9
Every structure of UniProt A0A077ULC5
Every structure of UniProt A0A077W1J5
Every structure of UniProt A0A077UL47
Every structure of UniProt A0A077V2P0
Every structure of UniProt W8TQ59
Every structure of UniProt A0A077UGV8
Every structure of UniProt W8U3W0
Every structure of UniProt A0A2S6D0C0
Every structure of UniProt A0A077UUA0
Every structure of UniProt A0A6I4H7Y4
Every structure of UniProt A0A077URJ8
Every structure of UniProt W8UVN7
Every structure of UniProt A0A1Q8DAT0
Every structure of UniProt A0A077UG91
Elsewhere: RCSB PDB 7ASM · PDBe 7ASM · UniProt A0A077UVB6 · UniProt W8TRC7 · UniProt B3VKN3 · UniProt W8U3X2 · UniProt W8TUE6 · UniProt A0A077UGA7 · UniProt A0A077V4G0 · UniProt W8TRE0 · UniProt A0A077VMP6 · UniProt D7URR3 · UniProt W8TUB4 · UniProt A0A6K7SSC4 · UniProt A0A133Q8Z9 · UniProt A0A077ULC5 · UniProt A0A077W1J5 · UniProt A0A077UL47 · UniProt A0A077V2P0 · UniProt W8TQ59 · UniProt A0A077UGV8 · UniProt W8U3W0 · UniProt A0A2S6D0C0 · UniProt A0A077UUA0 · UniProt A0A6I4H7Y4 · UniProt A0A077URJ8 · UniProt W8UVN7 · UniProt A0A1Q8DAT0 · UniProt A0A077UG91

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