MolNFT v2 · #159631 · protein + RNA

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

6NWY: “Modified tRNA(Pro) bound to Thermus thermophilus 70S (near-cognate)”. X-ray diffraction at 3.5, 3 ligands (SF4, MG, ZN). MolNFT v2 #159631 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

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
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

Structure

x-ray diffraction · resolution 3.5 · 71 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
QA	—	rna	1511	—	—
QB	—	protein	235	—	P80371
QC, XC	—	protein	205	—	P80372
QD, XD	—	protein	208	—	P80373
QE, XE	—	protein	151	—	Q5SHQ5
QF, XF	—	protein	101	—	Q5SLP8
QG, XG	—	protein	155	—	P17291
QH, XH	—	protein	137	—	P0DOY9
QI	—	protein	127	—	P80374
QJ	—	protein	99	—	Q5SHN7
QK	—	protein	119	—	P80376
QL	—	protein	125	—	Q5SHN3
QM	—	protein	120	—	P80377
QN, XN	—	protein	60	—	P0DOY6
QO	—	protein	88	—	Q5SJ76
QP, XP	—	protein	84	—	Q5SJH3
QQ, XQ	—	protein	100	—	P0DOY7
QR, XR	—	protein	70	—	Q5SLQ0
QS	—	protein	83	—	Q5SHP2
QT, XT	—	protein	99	—	P80380
QU, XU	—	protein	25	—	Q5SIH3
QV, XV	—	rna	77	—	—
QX, XX	—	rna	19	—	—
R0	—	protein	81	—	P60493
R1	—	protein	95	—	P60494
R2	—	protein	69	—	Q5SHP6
R3, Y3	—	protein	59	—	Q5SHQ6
R4	—	protein	45	—	Q5SJE1
R5, Y5	—	protein	59	—	P80339
R6, Y6	—	protein	53	—	P35871
R7	—	protein	47	—	P80340
R8, Y8	—	protein	64	—	Q5SKU1
R9, Y9	—	protein	37	—	Q5SHR2
RA	—	rna	2882	—	—
RB, YB	—	rna	120	—	—
RD, YD	—	protein	272	—	P60405
RE, YE	—	protein	205	—	Q5SHN8
RF, YF	—	protein	202	—	Q5SHN9
RG, YG	—	protein	181	—	Q5SHQ0
RH, YH	—	protein	174	—	P0DOY8
RI, YI	—	protein	146	—	Q5SLQ1
RN, YN	—	protein	138	—	P60488
RO, YO	—	protein	122	—	Q5SHP8
RP	—	protein	150	—	Q5SHQ7
RQ, YQ	—	protein	141	—	P60489
RR, YR	—	protein	117	—	Q9Z9H5
RS, YS	—	protein	111	—	Q5SHQ4
RT, YT	—	protein	137	—	P60490
RU, YU	—	protein	117	—	P60491
RV, YV	—	protein	101	—	P60492
RW, YW	—	protein	113	—	Q5SHP3
RX, YX	—	protein	92	—	Q5SHP0
RY, YY	—	protein	107	—	Q5SHP9
RZ	—	protein	183	—	Q5SHZ1
XA	—	rna	1515	—	—
XB	—	protein	236	—	P80371
XI	—	protein	126	—	P80374
XJ	—	protein	96	—	Q5SHN7
XK	—	protein	116	—	P80376
XL	—	protein	122	—	Q5SHN3
XM	—	protein	114	—	P80377
XO	—	protein	87	—	Q5SJ76
XS	—	protein	84	—	Q5SHP2
Y0	—	protein	82	—	P60493
Y1	—	protein	93	—	P60494
Y2	—	protein	68	—	Q5SHP6
Y4	—	protein	46	—	Q5SJE1
Y7	—	protein	48	—	P80340
YA	—	rna	2883	—	—
YP	—	protein	147	—	Q5SHQ7
YZ	—	protein	193	—	Q5SHZ1

Ligands and binding sites

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

Compared structures

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

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