Research workbench

Stm1 bound vacant 80S structure isolated from cbf5-D95A

Analyse Stm1 bound vacant 80S structure isolated from cbf5-D95A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MPI
Type: protein + RNA
Length: 16,318 residues
Chains: 79
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.05
Source: Saccharomyces cerevisiae
Molecule: 40S ribosomal protein S0-A; 40S ribosomal protein S1-A; 40S ribosomal protein S2; 40S…
UniProt: P32905, P33442, P25443, P05750, P0CX35, P26783, P0CX37, P26786, P0CX39, O13516, Q08745, P0CX47, P48589, P05756, P06367, Q01855, P0CX51, P02407, P0CX55, P07280, P38701, P0C0V8, P0C0W1, P0CX29, P0CX31, Q3E792, P39939, P35997, Q3E7X9, P41057, P0CX33, P05759, P38011, P39015, P0CX45, P14126, P10664, P26321, Q02326, P05737, P17076, P05738, P41805, P0C0W9, Q12690, P36105, P05748, P26784, P05740, P0CX49, P0CX82, P0CX23, Q02753, P05749, P0CX41, P04449, P04456, P05743, P0C2H6, P02406, P05747, P14120, P0C2H8, P38061, P05744, P87262, P0CX84, P05745, P49166, P49167, P04650, P0CH08, P0CX86, P0CX27, P0CX25
Ligands: MG, ZN
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · resolution 3.05 · 79 distinct chains · 29% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
BA	40S ribosomal protein S0-A	protein	206	31% helix, 14% strand	P32905
BB	40S ribosomal protein S1-A	protein	214	26% helix, 27% strand	P33442
BC	40S ribosomal protein S2	protein	217	29% helix, 25% strand	P25443
BD	40S ribosomal protein S3	protein	223	32% helix, 27% strand	P05750
BE	40S ribosomal protein S4-A	protein	260	16% helix, 28% strand	P0CX35
BF	40S ribosomal protein S5	protein	206	44% helix, 9% strand	P26783
BG	40S ribosomal protein S6-A	protein	226	23% helix, 25% strand	P0CX37
BH	40S ribosomal protein S7-A	protein	184	33% helix, 18% strand	P26786
BI	40S ribosomal protein S8-A	protein	188	26% helix, 22% strand	P0CX39
BJ	40S ribosomal protein S9-A	protein	185	45% helix, 2% strand	O13516
BK	40S ribosomal protein S10-A	protein	96	39% helix, 11% strand	Q08745
BL	40S ribosomal protein S11-A	protein	155	3% helix, 28% strand	P0CX47
BM	40S ribosomal protein S12	protein	121	24% helix, 9% strand	P48589
BN	40S ribosomal protein S13	protein	150	51% helix, 0% strand	P05756
BO	40S ribosomal protein S14-A	protein	127	22% helix, 21% strand	P06367
BP	40S ribosomal protein S15	protein	124	31% helix, 12% strand	Q01855
BQ	40S ribosomal protein S16-A	protein	141	34% helix, 20% strand	P0CX51
BR	40S ribosomal protein S17-A	protein	121	52% helix, 3% strand	P02407
BS	40S ribosomal protein S18-A	protein	145	34% helix, 4% strand	P0CX55
BT	40S ribosomal protein S19-A	protein	141	45% helix, 10% strand	P07280
BU	40S ribosomal protein S20	protein	107	22% helix, 40% strand	P38701
BV	40S ribosomal protein S21-A	protein	87	17% helix, 24% strand	P0C0V8
BW	40S ribosomal protein S22-A	protein	129	32% helix, 25% strand	P0C0W1
BX	40S ribosomal protein S23-A	protein	144	20% helix, 22% strand	P0CX29
BY	40S ribosomal protein S24-A	protein	134	35% helix, 25% strand	P0CX31
BZ	40S ribosomal protein S25-A	protein	69	42% helix, 16% strand	Q3E792
Ba	40S ribosomal protein S26-B	protein	97	12% helix, 22% strand	P39939
Bb	40S ribosomal protein S27-A	protein	81	5% helix, 20% strand	P35997
Bc	40S ribosomal protein S28-A	protein	63	0% helix, 48% strand	Q3E7X9
Bd	40S ribosomal protein S29-A	protein	53	19% helix, 9% strand	P41057
Be	40S ribosomal protein S30-A	protein	60	30% helix, 2% strand	P0CX33
Bf	40S ribosomal protein S31	protein	57	0% helix, 7% strand	P05759
Bg	Guanine nucleotide-binding protein subunit beta-like protein	protein	312	0% helix, 50% strand	P38011
Bh	Suppressor protein STM1	protein	89	47% helix, 0% strand	P39015
B5	18S rRNA	rna	1781	—	—
A1	25S rRNA	rna	3137	—	—
A3	5s rRNA	rna	121	—	—
A4	5.8 S rRNA	rna	158	—	—
AA	60S ribosomal protein L2-A	protein	247	9% helix, 27% strand	P0CX45
AB	60S ribosomal protein L3	protein	386	15% helix, 27% strand	P14126
AC	60S ribosomal protein L4-A	protein	361	29% helix, 10% strand	P10664
AD	60S ribosomal protein L5	protein	292	39% helix, 11% strand	P26321
AE	60S ribosomal protein L6-A	protein	156	17% helix, 17% strand	Q02326
AF	60S ribosomal protein L7-A	protein	222	50% helix, 13% strand	P05737
AG	60S ribosomal protein L8-A	protein	230	48% helix, 8% strand	P17076
AH	60S ribosomal protein L9-A	protein	190	21% helix, 42% strand	P05738
AI	60S ribosomal protein L10	protein	205	22% helix, 26% strand	P41805
AJ	60S ribosomal protein L11-A	protein	169	20% helix, 21% strand	P0C0W9
AL	60S ribosomal protein L13-A	protein	193	39% helix, 9% strand	Q12690
AM	60S ribosomal protein L14-A	protein	136	42% helix, 26% strand	P36105
AN	60S ribosomal protein L15-A	protein	203	39% helix, 18% strand	P05748
AO	60S ribosomal protein L16-A	protein	197	52% helix, 12% strand	P26784
AP	60S ribosomal protein L17-A	protein	175	35% helix, 28% strand	P05740
AQ	60S ribosomal protein L18-A	protein	185	29% helix, 15% strand	P0CX49
AR	60S ribosomal protein L19-A	protein	188	61% helix, 2% strand	P0CX82
AS	60S ribosomal protein L20-A	protein	172	22% helix, 31% strand	P0CX23
AT	60S ribosomal protein L21-A	protein	159	20% helix, 23% strand	Q02753
AU	60S ribosomal protein L22-A	protein	100	29% helix, 30% strand	P05749
AV	60S ribosomal protein L23-A	protein	136	9% helix, 33% strand	P0CX41
AW	60S ribosomal protein L24-A	protein	63	27% helix, 17% strand	P04449
AX	60S ribosomal protein L25	protein	121	26% helix, 21% strand	P04456
AY	60S ribosomal protein L26-A	protein	126	30% helix, 32% strand	P05743
AZ	60S ribosomal protein L27-A	protein	135	21% helix, 27% strand	P0C2H6
Aa	60S ribosomal protein L28	protein	148	19% helix, 14% strand	P02406
Ab	60S ribosomal protein L29	protein	58	50% helix, 2% strand	P05747
Ac	60S ribosomal protein L30	protein	97	40% helix, 16% strand	P14120
Ad	60S ribosomal protein L31-A	protein	109	28% helix, 28% strand	P0C2H8
Ae	60S ribosomal protein L32	protein	127	17% helix, 9% strand	P38061
Af	60S ribosomal protein L33-A	protein	106	4% helix, 49% strand	P05744
Ag	60S ribosomal protein L34-A	protein	112	32% helix, 11% strand	P87262
Ah	60S ribosomal protein L35-A	protein	119	56% helix, 3% strand	P0CX84
Ai	60S ribosomal protein L36-A	protein	99	56% helix, 1% strand	P05745
Aj	60S ribosomal protein L37-A	protein	87	22% helix, 7% strand	P49166
Ak	60S ribosomal protein L38	protein	77	19% helix, 34% strand	P49167
Al	60S ribosomal protein L39	protein	50	30% helix, 0% strand	P04650
Am	60S ribosomal protein L40-A	protein	52	21% helix, 15% strand	P0CH08
An	60S ribosomal protein L41-A	protein	25	84% helix, 0% strand	P0CX86
Ao	60S ribosomal protein L42-A	protein	105	10% helix, 28% strand	P0CX27
Ap	60S ribosomal protein L43-A	protein	91	42% helix, 15% strand	P0CX25

Ligands and binding sites

MG · Magnesium ion · metal · 366 copies · chains BD, B5, BJ, BL, Bd, BT, BE, BX, BS, Bc, BQ, BN, Bh, BG, Ba, A1, A4, AB, AN, Aj, Ai, Ag, AP, Af, AX, Ad, AL, AR, Aa, AA, Ae, Ab, AO, AC, AI, Al, A3, AH, AT, Ah, AG, Ao
ZN · Zinc ion · metal · 2 copies · chains Bb, Ao

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	994	0.90	0.93	103	MG
2	933	0.90	0.93	106	MG
3	1060	0.89	0.92	104	MG
4	1091	0.89	0.91	107	MG
5	989	0.89	0.91	95	MG

Interfaces

245 interfaces between chains.

A1–AB · 9189 Å² buried · 233 hydrogen bonds · protein-nucleic
A1–AC · 8422 Å² buried · 192 hydrogen bonds · protein-nucleic
A1–AN · 7430 Å² buried · 176 hydrogen bonds · protein-nucleic
A1–AA · 7323 Å² buried · 189 hydrogen bonds · protein-nucleic
BG–B5 · 5449 Å² buried · 158 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 66 modified (nucleotide modification, methylation).

Compared structures

P0CX45 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L2-a (P0CX45) · a predicted model of the same protein · chain AA against A, TM-score 0.99
P25443 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S2 (P25443) · a predicted model of the same protein · chain BC against A, TM-score 0.99
P38011 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein subunit… · a predicted model of the same protein · chain Bg against A, TM-score 0.98
P07280 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S19-a (P07280) · a predicted model of the same protein · chain BT against A, TM-score 0.98
P0CX25 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L43-a (P0CX25) · a predicted model of the same protein · chain Ap against A, TM-score 0.98
P26784 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L16-a (P26784) · a predicted model of the same protein · chain AO against A, TM-score 0.98
P38061 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L32 (P38061) · a predicted model of the same protein · chain Ae against A, TM-score 0.98
P41805 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L10 (P41805) · a predicted model of the same protein · chain AI against A, TM-score 0.98
P32905 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S0-a (P32905) · a predicted model of the same protein · chain BA against A, TM-score 0.98
P0C0W1 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S22-a (P0C0W1) · a predicted model of the same protein · chain BW against A, TM-score 0.98
P06367 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S14-a (P06367) · a predicted model of the same protein · chain BO against A, TM-score 0.98
P26783 · AlphaFold monomer V2.0 prediction for 40S ribosomal protein S5 (P26783) · a predicted model of the same protein · chain BF against A, TM-score 0.98

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