GL1X · GenesisL1 explorer

MolNFT v2 · #187219 · protein + RNA

Stm1 bound vacant 80S structure isolated from cbf5-D95A

7MPI: “Stm1 bound vacant 80S structure isolated from cbf5-D95A”. Electron microscopy at 3.05, 2 ligands (MG, ZN). MolNFT v2 #187219 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

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
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

Structure

electron microscopy · resolution 3.05 · 79 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
BA—protein206—P32905
BB—protein214—P33442
BC—protein217—P25443
BD—protein223—P05750
BE—protein260—P0CX35
BF—protein206—P26783
BG—protein226—P0CX37
BH—protein184—P26786
BI—protein188—P0CX39
BJ—protein185—O13516
BK—protein96—Q08745
BL—protein155—P0CX47
BM—protein121—P48589
BN—protein150—P05756
BO—protein127—P06367
BP—protein124—Q01855
BQ—protein141—P0CX51
BR—protein121—P02407
BS—protein145—P0CX55
BT—protein141—P07280
BU—protein107—P38701
BV—protein87—P0C0V8
BW—protein129—P0C0W1
BX—protein144—P0CX29
BY—protein134—P0CX31
BZ—protein69—Q3E792
Ba—protein97—P39939
Bb—protein81—P35997
Bc—protein63—Q3E7X9
Bd—protein53—P41057
Be—protein60—P0CX33
Bf—protein57—P05759
Bg—protein312—P38011
Bh—protein89—P39015
B5—rna1781——
A1—rna3137——
A3—rna121——
A4—rna158——
AA—protein247—P0CX45
AB—protein386—P14126
AC—protein361—P10664
AD—protein292—P26321
AE—protein156—Q02326
AF—protein222—P05737
AG—protein230—P17076
AH—protein190—P05738
AI—protein205—P41805
AJ—protein169—P0C0W9
AL—protein193—Q12690
AM—protein136—P36105
AN—protein203—P05748
AO—protein197—P26784
AP—protein175—P05740
AQ—protein185—P0CX49
AR—protein188—P0CX82
AS—protein172—P0CX23
AT—protein159—Q02753
AU—protein100—P05749
AV—protein136—P0CX41
AW—protein63—P04449
AX—protein121—P04456
AY—protein126—P05743
AZ—protein135—P0C2H6
Aa—protein148—P02406
Ab—protein58—P05747
Ac—protein97—P14120
Ad—protein109—P0C2H8
Ae—protein127—P38061
Af—protein106—P05744
Ag—protein112—P87262
Ah—protein119—P0CX84
Ai—protein99—P05745
Aj—protein87—P49166
Ak—protein77—P49167
Al—protein50—P04650
Am—protein52—P0CH08
An—protein25—P0CX86
Ao—protein105—P0CX27
Ap—protein91—P0CX25

Ligands and binding sites

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

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

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
  • 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
  • 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
  • P05743 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L26-a (P05743) · a predicted model of the same protein · chain AY against A, TM-score 0.98
  • P0CX49 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L18-a (P0CX49) · a predicted model of the same protein · chain AQ against A, TM-score 0.97
  • P14120 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L30 (P14120) · a predicted model of the same protein · chain Ac against A, TM-score 0.97
  • P02406 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L28 (P02406) · a predicted model of the same protein · chain Aa against A, TM-score 0.97
  • P05744 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L33-a (P05744) · a predicted model of the same protein · chain Af against A, TM-score 0.97
  • P0C2H8 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L31-a (P0C2H8) · a predicted model of the same protein · chain Ad against A, TM-score 0.96
  • Q02753 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L21-a (Q02753) · a predicted model of the same protein · chain AT against A, TM-score 0.96
  • P36105 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L14-a (P36105) · a predicted model of the same protein · chain AM against A, TM-score 0.94

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