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Structure of rabbit 80S ribosome translating beta-tubulin in complex with tetratricopeptide protein 5 and nascent chain-associated complex

Analyse Structure of rabbit 80S ribosome translating beta-tubulin in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6T59
Type: protein + RNA
Length: 11,273 residues
Chains: 53
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.11
Source: Homo sapiens; Oryctolagus cuniculus
Molecule: Ribosomal protein L8; uL3; uL4; 60S ribosomal protein L5; 60S ribosomal protein L6; Ul30…
UniProt: G1TT27, G1TL06, G1SYJ6, G1SKF7, G1TUB1, G1TX33, B7NZQ2, G1TUB8, G1SZ12, G1T0C1, G1TVT6, G1SHQ2, G1T6D1, G1SE28, G1SE76, G1SQH0, G1TXF6, G1SNY0, G1SGR6, G1TDL2, G1SHG0, G1U437, G1SF08, G1U945, G1SIT5, G1TTQ5, U3KPD5, G1U001, G1TTN1, A0A087WNH4, G1U344, G1SY53, G1U7L1, G1SMR7, Q8N0Z6
Ligands: MG, ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · resolution 3.11 · 53 distinct chains · 30% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A3	Ribosomal protein L8	protein	248	9% helix, 24% strand	G1TT27
B3	uL3	protein	394	13% helix, 26% strand	G1TL06
C3	uL4	protein	362	33% helix, 10% strand	—
D3	60S ribosomal protein L5	protein	293	42% helix, 9% strand	G1SYJ6
E3	60S ribosomal protein L6	protein	216	19% helix, 17% strand	G1SKF7
F3	Ul30	protein	225	51% helix, 16% strand	G1TUB1
G3	eL8	protein	233	45% helix, 8% strand	—
H3	uL6	protein	190	22% helix, 35% strand	G1TX33
I3	60S ribosomal protein L10	protein	205	23% helix, 27% strand	B7NZQ2
J3	Ribosomal protein L11	protein	170	26% helix, 24% strand	G1TUB8
L3	eL13	protein	210	34% helix, 7% strand	—
M3	Ribosomal protein L14	protein	138	46% helix, 25% strand	G1SZ12
N3	Ribosomal protein L15	protein	203	31% helix, 16% strand	G1T0C1
O3	uL13	protein	199	46% helix, 10% strand	—
P3	uL22	protein	153	31% helix, 27% strand	G1TVT6
Q3	eL18	protein	187	25% helix, 10% strand	—
R3	eL19	protein	155	54% helix, 4% strand	—
S3	eL20	protein	176	20% helix, 26% strand	—
T3	eL21	protein	159	14% helix, 23% strand	G1SHQ2
U3	eL22	protein	102	30% helix, 29% strand	—
V3	Ribosomal protein L23	protein	131	8% helix, 34% strand	G1T6D1
W3	eL24	protein	63	24% helix, 24% strand	G1SE28
X3	uL23	protein	118	20% helix, 22% strand	G1SE76
Y3	Ribosomal protein L26	protein	134	31% helix, 25% strand	G1SQH0
Z3	60S ribosomal protein L27	protein	135	27% helix, 27% strand	G1TXF6
a3	uL15	protein	147	21% helix, 14% strand	G1SNY0
b3	eL29	protein	104	58% helix, 0% strand	G1SGR6
c3	eL30	protein	98	42% helix, 18% strand	G1TDL2
d3	eL31	protein	107	28% helix, 22% strand	G1SHG0
e3	eL32	protein	128	18% helix, 8% strand	G1U437
f3	eL33	protein	109	3% helix, 51% strand	G1SF08
g3	eL34	protein	114	34% helix, 9% strand	G1U945
h3	uL29	protein	122	59% helix, 2% strand	G1SIT5
i3	60S ribosomal protein L36	protein	102	46% helix, 0% strand	G1TTQ5
j3	Ribosomal protein L37	protein	86	21% helix, 7% strand	U3KPD5
k3	eL38	protein	69	23% helix, 32% strand	G1U001
l3	eL39	protein	50	30% helix, 0% strand	G1TTN1
m3	eL40	protein	52	21% helix, 15% strand	—
n3	60s ribosomal protein l41	protein	25	80% helix, 0% strand	A0A087WNH4
o3	eL42	protein	104	9% helix, 30% strand	G1U344
p3	eL43	protein	91	40% helix, 11% strand	G1SY53
r3	eL28	protein	124	30% helix, 21% strand	G1U7L1
s3	uL10	protein	196	23% helix, 8% strand	—
t3	Ribosomal protein L12	protein	153	33% helix, 7% strand	G1SMR7
23	P-site tRNA	rna	76	—	—
54	28S ribosomal RNA	rna	3543	—	—
74	5S ribosomal RNA	rna	120	—	—
84	5.8S ribosomal RNA	rna	151	—	—
NI	Nascent polypeptide-associated complex subunit alpha N-terminal region	protein	29	31% helix, 3% strand	—
NA	Nascent polypeptide-associated complex subunit alpha	protein	54	0% helix, 24% strand	—
NB	Transcription factor BTF3	protein	58	7% helix, 38% strand	—
TT	Tetratricopeptide repeat protein 5	protein	426	53% helix, 10% strand	Q8N0Z6
1	Tubulin Beta	protein	36	0% helix, 0% strand	—

Ligands and binding sites

MG · Magnesium ion · metal · 220 copies · chains P3, 54, V3, a3, g3, j3, B3, I3, Q3, e3, C3, N3, 84, A3, H3, F3, L3, b3, O3, X3, 74
ZN · Zinc ion · metal · 5 copies · chains g3, j3, m3, o3, p3

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	1146	0.89	0.92	123	MG
2	796	0.88	0.93	99	MG
3	969	0.88	0.90	91	empty
4	952	0.88	0.90	90	MG
5	873	0.88	0.91	91	MG

Interfaces

156 interfaces between chains.

C3–54 · 9689 Å² buried · 168 hydrogen bonds · protein-nucleic
B3–54 · 9188 Å² buried · 198 hydrogen bonds · protein-nucleic
A3–54 · 7622 Å² buried · 170 hydrogen bonds · protein-nucleic
N3–54 · 7055 Å² buried · 127 hydrogen bonds · protein-nucleic
E3–54 · 5938 Å² buried · 100 hydrogen bonds · protein-nucleic

Compared structures

Q8N0Z6 · AlphaFold monomer V2.0 prediction for tetratricopeptide repeat protein 5 (Q8N0Z6) · a predicted model of the same protein · chain TT against A, TM-score 0.97

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 G1TT27
Every structure of UniProt G1TL06
Every structure of UniProt G1SYJ6
Every structure of UniProt G1SKF7
Every structure of UniProt G1TUB1
Every structure of UniProt G1TX33
Every structure of UniProt B7NZQ2
Every structure of UniProt G1TUB8
Every structure of UniProt G1SZ12
Every structure of UniProt G1T0C1
Every structure of UniProt G1TVT6
Every structure of UniProt G1SHQ2
Every structure of UniProt G1T6D1
Every structure of UniProt G1SE28
Every structure of UniProt G1SE76
Every structure of UniProt G1SQH0
Every structure of UniProt G1TXF6
Every structure of UniProt G1SNY0
Every structure of UniProt G1SGR6
Every structure of UniProt G1TDL2
Every structure of UniProt G1SHG0
Every structure of UniProt G1U437
Every structure of UniProt G1SF08
Every structure of UniProt G1U945
Every structure of UniProt G1SIT5
Every structure of UniProt G1TTQ5
Every structure of UniProt U3KPD5
Every structure of UniProt G1U001
Every structure of UniProt G1TTN1
Every structure of UniProt A0A087WNH4
Every structure of UniProt G1U344
Every structure of UniProt G1SY53
Every structure of UniProt G1U7L1
Every structure of UniProt G1SMR7
Every structure of UniProt Q8N0Z6
Elsewhere: RCSB PDB 6T59 · PDBe 6T59 · UniProt G1TT27 · UniProt G1TL06 · UniProt G1SYJ6 · UniProt G1SKF7 · UniProt G1TUB1 · UniProt G1TX33 · UniProt B7NZQ2 · UniProt G1TUB8 · UniProt G1SZ12 · UniProt G1T0C1 · UniProt G1TVT6 · UniProt G1SHQ2 · UniProt G1T6D1 · UniProt G1SE28 · UniProt G1SE76 · UniProt G1SQH0 · UniProt G1TXF6 · UniProt G1SNY0 · UniProt G1SGR6 · UniProt G1TDL2 · UniProt G1SHG0 · UniProt G1U437 · UniProt G1SF08 · UniProt G1U945 · UniProt G1SIT5 · UniProt G1TTQ5 · UniProt U3KPD5 · UniProt G1U001 · UniProt G1TTN1 · UniProt A0A087WNH4 · UniProt G1U344 · UniProt G1SY53 · UniProt G1U7L1 · UniProt G1SMR7 · UniProt Q8N0Z6

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