Research workbench

Modified tRNA(Pro) bound to Thermus thermophilus 70S (near-cognate)

Analyse Modified tRNA(Pro) bound to Thermus thermophilus 70S (near-cognate) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NWY
Type: protein + RNA
Length: 20,833 residues
Chains: 108
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.5
Source: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579); SYNTHETIC CONSTRUCT
Molecule: 16S rRNA; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S ribosomal protein S4…
UniProt: P80371, P80372, P80373, Q5SHQ5, Q5SLP8, P17291, P0DOY9, P80374, Q5SHN7, P80376, Q5SHN3, P80377, P0DOY6, Q5SJ76, Q5SJH3, P0DOY7, Q5SLQ0, Q5SHP2, P80380, Q5SIH3, P60493, P60494, Q5SHP6, Q5SHQ6, Q5SJE1, P80339, P35871, P80340, Q5SKU1, Q5SHR2, P60405, Q5SHN8, Q5SHN9, Q5SHQ0, P0DOY8, Q5SLQ1, P60488, Q5SHP8, Q5SHQ7, P60489, Q9Z9H5, Q5SHQ4, P60490, P60491, P60492, Q5SHP3, Q5SHP0, Q5SHP9, Q5SHZ1
Ligands: SF4, MG, ZN
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · resolution 3.5 · 71 distinct chains · 26% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
QA	16S rRNA	rna	1511	—	—
QB	30S ribosomal protein S2	protein	235	41% helix, 12% strand	P80371
QC, XC	30S ribosomal protein S3	protein	205	36% helix, 27% strand	P80372
QD, XD	30S ribosomal protein S4	protein	208	40% helix, 8% strand	P80373
QE, XE	30S ribosomal protein S5	protein	151	28% helix, 36% strand	Q5SHQ5
QF, XF	30S ribosomal protein S6	protein	101	27% helix, 41% strand	Q5SLP8
QG, XG	30S ribosomal protein S7	protein	155	50% helix, 9% strand	P17291
QH, XH	30S ribosomal protein S8	protein	137	30% helix, 31% strand	P0DOY9
QI	30S ribosomal protein S9	protein	127	21% helix, 20% strand	P80374
QJ	30S ribosomal protein S10	protein	99	24% helix, 39% strand	Q5SHN7
QK	30S ribosomal protein S11	protein	119	31% helix, 24% strand	P80376
QL	30S ribosomal protein S12	protein	125	7% helix, 23% strand	Q5SHN3
QM	30S ribosomal protein S13	protein	120	47% helix, 2% strand	P80377
QN, XN	30S ribosomal protein S14 type Z	protein	60	27% helix, 5% strand	P0DOY6
QO	30S ribosomal protein S15	protein	88	76% helix, 0% strand	Q5SJ76
QP, XP	30S ribosomal protein S16	protein	84	24% helix, 36% strand	Q5SJH3
QQ, XQ	30S ribosomal protein S17	protein	100	16% helix, 51% strand	P0DOY7
QR, XR	30S ribosomal protein S18	protein	70	30% helix, 7% strand	Q5SLQ0
QS	30S ribosomal protein S19	protein	83	14% helix, 18% strand	Q5SHP2
QT, XT	30S ribosomal protein S20	protein	99	69% helix, 0% strand	P80380
QU, XU	30S ribosomal protein Thx	protein	25	24% helix, 0% strand	Q5SIH3
QV, XV	E-site tRNA-Pro	rna	77	—	—
QX, XX	mRNA	rna	19	—	—
R0	50S ribosomal protein L27	protein	81	4% helix, 37% strand	P60493
R1	50S ribosomal protein L28	protein	95	11% helix, 31% strand	P60494
R2	50S ribosomal protein L29	protein	69	78% helix, 0% strand	Q5SHP6
R3, Y3	50S ribosomal protein L30	protein	59	32% helix, 20% strand	Q5SHQ6
R4	50S ribosomal protein L31	protein	45	0% helix, 33% strand	Q5SJE1
R5, Y5	50S ribosomal protein L32	protein	59	10% helix, 17% strand	P80339
R6, Y6	50S ribosomal protein L33	protein	53	0% helix, 57% strand	P35871
R7	50S ribosomal protein L34	protein	47	51% helix, 0% strand	P80340
R8, Y8	50S ribosomal protein L35	protein	64	14% helix, 14% strand	Q5SKU1
R9, Y9	50S ribosomal protein L36	protein	37	8% helix, 43% strand	Q5SHR2
RA	23S rRNA	rna	2882	—	—
RB, YB	5S rRNA	rna	120	—	—
RD, YD	50S ribosomal protein L2	protein	272	5% helix, 22% strand	P60405
RE, YE	50S ribosomal protein L3	protein	205	1% helix, 27% strand	Q5SHN8
RF, YF	50S ribosomal protein L4	protein	202	27% helix, 13% strand	Q5SHN9
RG, YG	50S ribosomal protein L5	protein	181	30% helix, 16% strand	Q5SHQ0
RH, YH	50S ribosomal protein L6	protein	174	18% helix, 26% strand	P0DOY8
RI, YI	50S ribosomal protein L9	protein	146	36% helix, 20% strand	Q5SLQ1
RN, YN	50S ribosomal protein L13	protein	138	22% helix, 15% strand	P60488
RO, YO	50S ribosomal protein L14	protein	122	7% helix, 36% strand	Q5SHP8
RP	50S ribosomal protein L15	protein	150	15% helix, 9% strand	Q5SHQ7
RQ, YQ	50S ribosomal protein L16	protein	141	18% helix, 16% strand	P60489
RR, YR	50S ribosomal protein L17	protein	117	52% helix, 14% strand	Q9Z9H5
RS, YS	50S ribosomal protein L18	protein	111	37% helix, 20% strand	Q5SHQ4
RT, YT	50S ribosomal protein L19	protein	137	19% helix, 33% strand	P60490
RU, YU	50S ribosomal protein L20	protein	117	71% helix, 0% strand	P60491
RV, YV	50S ribosomal protein L21	protein	101	0% helix, 56% strand	P60492
RW, YW	50S ribosomal protein L22	protein	113	36% helix, 34% strand	Q5SHP3
RX, YX	50S ribosomal protein L23	protein	92	24% helix, 32% strand	Q5SHP0
RY, YY	50S ribosomal protein L24	protein	107	0% helix, 43% strand	Q5SHP9
RZ	50S ribosomal protein L25	protein	183	10% helix, 36% strand	Q5SHZ1
XA	16S rRNA	rna	1515	—	—
XB	30S ribosomal protein S2	protein	236	40% helix, 12% strand	P80371
XI	30S ribosomal protein S9	protein	126	29% helix, 21% strand	P80374
XJ	30S ribosomal protein S10	protein	96	24% helix, 28% strand	Q5SHN7
XK	30S ribosomal protein S11	protein	116	32% helix, 26% strand	P80376
XL	30S ribosomal protein S12	protein	122	5% helix, 25% strand	Q5SHN3
XM	30S ribosomal protein S13	protein	114	45% helix, 2% strand	P80377
XO	30S ribosomal protein S15	protein	87	77% helix, 0% strand	Q5SJ76
XS	30S ribosomal protein S19	protein	84	8% helix, 17% strand	Q5SHP2
Y0	50S ribosomal protein L27	protein	82	4% helix, 38% strand	P60493
Y1	50S ribosomal protein L28	protein	93	8% helix, 35% strand	P60494
Y2	50S ribosomal protein L29	protein	68	74% helix, 0% strand	Q5SHP6
Y4	50S ribosomal protein L31	protein	46	0% helix, 9% strand	Q5SJE1
Y7	50S ribosomal protein L34	protein	48	52% helix, 0% strand	P80340
YA	23S rRNA	rna	2883	—	—
YP	50S ribosomal protein L15	protein	147	9% helix, 8% strand	Q5SHQ7
YZ	50S ribosomal protein L25	protein	193	9% helix, 36% strand	Q5SHZ1

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 2 copies · chains QD, XD
MG · Magnesium ion · metal · 1098 copies · chains QA, RA, QD, QT, QE, RO, QF, QH, QL, R0, RQ, R1, R3, R8, RP, QO, RE, RY, RF, RU, RV, R5, RD, RX, RW, RR, RN, RT, RB, R4, XA, YA, XC, XT, XD, XO, XE, Y1, Y2, Y5, Y7, Y8, YP, YQ, YD, YV, YN, Y3, YY, YF, YX, YW, YR, YU, YE, Y9, Y0, YB
ZN · Zinc ion · metal · 10 copies · chains QN, R5, R6, R9, RY, XN, Y5, Y6, Y9, YY

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	1807	0.89	0.92	164	MG
2	1912	0.89	0.91	159	MG
3	1844	0.88	0.91	147	MG
4	1020	0.88	0.91	86	MG
5	1609	0.88	0.91	112	MG

Interfaces

252 interfaces between chains.

YA–YD · 7484 Å² buried · 168 hydrogen bonds · protein-nucleic
RA–RD · 7431 Å² buried · 183 hydrogen bonds · protein-nucleic
YA–YE · 5193 Å² buried · 103 hydrogen bonds · protein-nucleic
RA–RE · 5188 Å² buried · 98 hydrogen bonds · protein-nucleic
YA–YP · 5171 Å² buried · 107 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 3 disulfide, 2 modified, 1 covalent (disulfide, nucleotide modification, covalent ligand).

Compared structures

P0DOY9 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S8 (P0DOY9) · a predicted model of the same protein · chain QH against A, TM-score 0.97
P0DOY8 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L6 (P0DOY8) · a predicted model of the same protein · chain RH against A, TM-score 0.95
Q5SHR2 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L36 (Q5SHR2) · a predicted model of the same protein · chain R9 against A, TM-score 0.93
P0DOY7 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S17 (P0DOY7) · a predicted model of the same protein · chain QQ against A, TM-score 0.92
P0DOY6 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S14 type Z (P0DOY6) · a predicted model of the same protein · chain QN against A, TM-score 0.86

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