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Molecular basis for the ribosome functioning as a L-tryptophan sensor - cryo-EM structure of a tnac stalled E.COLI ribosome

Analyse Molecular basis for the ribosome functioning as a L-tryptophan sensor - cryo-EM… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4UY8
Type: protein + RNA
Length: 6,515 residues
Chains: 35
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 50S ribosomal protein L32; 50S ribosomal protein L33; 50S ribosomal protein L34; 50S…
UniProt: U5SG25, U5SML7, P0A7P5, W0KX84, X7QRM8, E1IXH4, V5UZV4, A4GWE7, E3PCX7, X7QS81, D6IEL8, X7QRP4, X7QU92, X7QBP9, D8BKG3, E7HV64, X7QR95, E1PGS6, P02413, D7XL00, X7QRM3, X7QRN2, X7R0V6, X7QXR5, W0L2B9, E1JB10, C6EGE8, W0L2N0, W0KYJ4, C3SME2, D7X2Z3, W0L301
Ligands: TRP, MG, ZN
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 35 distinct chains · 24% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	50S ribosomal protein L32	protein	56	18% helix, 18% strand	U5SG25
1	50S ribosomal protein L33	protein	50	0% helix, 48% strand	U5SML7
2	50S ribosomal protein L34	protein	46	54% helix, 0% strand	P0A7P5
3	50S ribosomal protein L35	protein	64	27% helix, 3% strand	W0KX84
4	50S ribosomal protein L36	protein	38	8% helix, 29% strand	X7QRM8
5	50S ribosomal protein L10	protein	148	36% helix, 3% strand	E1IXH4
6	Ribosomal L7 protein	protein	30	37% helix, 0% strand	V5UZV4
7	Tryptophanase	protein	20	0% helix, 0% strand	A4GWE7
8	50S ribosomal protein L25	protein	94	22% helix, 43% strand	E3PCX7
A	RRNA-23S ribosomal RNA	rna	2854	—	—
B	RRNA-5S ribosomal RNA	rna	118	—	—
C	50S ribosomal protein L2	protein	271	8% helix, 20% strand	X7QS81
D	50S ribosomal protein L3	protein	209	7% helix, 25% strand	D6IEL8
E	50S ribosomal protein L4	protein	201	31% helix, 4% strand	X7QRP4
F	50S ribosomal protein L5	protein	177	36% helix, 16% strand	X7QU92
G	50S ribosomal protein L6	protein	176	18% helix, 23% strand	X7QBP9
H	Ribosomal protein L9	protein	50	28% helix, 10% strand	D8BKG3
I	50S ribosomal protein L11	protein	141	18% helix, 4% strand	E7HV64
J	50S ribosomal protein L13	protein	142	32% helix, 14% strand	X7QR95
K	50S ribosomal protein L14	protein	122	9% helix, 35% strand	E1PGS6
L	50S ribosomal protein L15	protein	143	15% helix, 10% strand	P02413
M	50S ribosomal protein L16	protein	136	20% helix, 21% strand	D7XL00
N	50S ribosomal protein L17	protein	120	48% helix, 13% strand	X7QRM3
O	50S ribosomal protein L18	protein	116	41% helix, 16% strand	X7QRN2
P	50S ribosomal protein L19	protein	114	18% helix, 32% strand	X7R0V6
Q	50S ribosomal protein L20	protein	117	76% helix, 0% strand	X7QXR5
R	50S ribosomal protein L21	protein	103	0% helix, 54% strand	W0L2B9
S	50S ribosomal protein L22	protein	110	29% helix, 32% strand	E1JB10
T	50S ribosomal protein L23	protein	93	19% helix, 18% strand	C6EGE8
U	50S ribosomal protein L24	protein	102	3% helix, 39% strand	W0L2N0
V	RNA	rna	77	—	—
W	50S ribosomal protein L27	protein	79	0% helix, 10% strand	W0KYJ4
X	50S ribosomal protein L28	protein	77	22% helix, 21% strand	C3SME2
Y	50S ribosomal protein L29	protein	63	67% helix, 0% strand	D7X2Z3
Z	50S ribosomal protein L30	protein	58	38% helix, 17% strand	W0L301

Ligands and binding sites

TRP · Tryptophan · ligand · 2 copies · chains 7, A
MG · Magnesium ion · metal · 143 copies · chains 4, A, E, L, C, Q, R, D, 3, T, J, B, 8
ZN · Zinc ion · metal · chains 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	934	0.87	0.90	84	MG
2	1137	0.87	0.89	119	MG
3	1078	0.87	0.89	88	MG
4	541	0.85	0.92	64	MG
5	555	0.84	0.91	73	empty

Interfaces

68 interfaces between chains.

A–C · 7194 Å² buried · 212 hydrogen bonds · protein-nucleic
A–D · 5014 Å² buried · 112 hydrogen bonds · protein-nucleic
A–L · 4479 Å² buried · 126 hydrogen bonds · protein-nucleic
A–E · 4215 Å² buried · 96 hydrogen bonds · protein-nucleic
A–Q · 4141 Å² buried · 110 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 3 disulfide, 1 modified (disulfide, nucleotide modification).

Compared structures

4UY8 · Molecular basis for the ribosome functioning as a L-tryptophan sensor - Cryo-EM structure… · the same entry in another collection · chain 1 against 1, 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 U5SG25
Every structure of UniProt U5SML7
Every structure of UniProt P0A7P5
Every structure of UniProt W0KX84
Every structure of UniProt X7QRM8
Every structure of UniProt E1IXH4
Every structure of UniProt V5UZV4
Every structure of UniProt A4GWE7
Every structure of UniProt E3PCX7
Every structure of UniProt X7QS81
Every structure of UniProt D6IEL8
Every structure of UniProt X7QRP4
Every structure of UniProt X7QU92
Every structure of UniProt X7QBP9
Every structure of UniProt D8BKG3
Every structure of UniProt E7HV64
Every structure of UniProt X7QR95
Every structure of UniProt E1PGS6
Every structure of UniProt P02413
Every structure of UniProt D7XL00
Every structure of UniProt X7QRM3
Every structure of UniProt X7QRN2
Every structure of UniProt X7R0V6
Every structure of UniProt X7QXR5
Every structure of UniProt W0L2B9
Every structure of UniProt E1JB10
Every structure of UniProt C6EGE8
Every structure of UniProt W0L2N0
Every structure of UniProt W0KYJ4
Every structure of UniProt C3SME2
Every structure of UniProt D7X2Z3
Every structure of UniProt W0L301
Elsewhere: RCSB PDB 4UY8 · PDBe 4UY8 · UniProt U5SG25 · UniProt U5SML7 · UniProt P0A7P5 · UniProt W0KX84 · UniProt X7QRM8 · UniProt E1IXH4 · UniProt V5UZV4 · UniProt A4GWE7 · UniProt E3PCX7 · UniProt X7QS81 · UniProt D6IEL8 · UniProt X7QRP4 · UniProt X7QU92 · UniProt X7QBP9 · UniProt D8BKG3 · UniProt E7HV64 · UniProt X7QR95 · UniProt E1PGS6 · UniProt P02413 · UniProt D7XL00 · UniProt X7QRM3 · UniProt X7QRN2 · UniProt X7R0V6 · UniProt X7QXR5 · UniProt W0L2B9 · UniProt E1JB10 · UniProt C6EGE8 · UniProt W0L2N0 · UniProt W0KYJ4 · UniProt C3SME2 · UniProt D7X2Z3 · UniProt W0L301

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