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MolNFT v2 · #151575 · protein + RNA

tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)

6GZ5: “tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis…”. Electron microscopy at 3.5, 3 ligands (GNP, MG, ZN). MolNFT v2 #151575 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
6GZ5
Type
protein + RNA
Length
18,458 residues
Chains
86
Method
electron microscopy
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
3.5
Source
Enterobacteria phage SP6; Oryctolagus cuniculus; Saccharomyces cerevisiae
Ligands
GNP, MG, ZN

Structure

electron microscopy · resolution 3.5 · 86 distinct chains.

ChainMoleculeTypeResiduesSecondary structureUniProt
A2—rna3612——
Bv—rna76——
Bx—rna11——
Bw—rna76——
B1—rna1708——
BD—protein220——
BF—protein190——
BK—protein98——
BM—protein120——
BP—protein120——
BQ—protein139——
BR—protein125——
BS—protein139——
BT—protein143——
BU—protein97——
BZ—protein86——
Bc—protein62——
Bd—protein51——
Bf—protein73——
Bg—protein314——
BA—protein215——
BB—protein212——
BC—protein222——
BE—protein257——
BG—protein232——
BH—protein183——
BI—protein207——
BJ—protein179——
BL—protein153——
BN—protein149——
BO—protein136——
BV—protein81——
BW—protein129——
BX—protein141——
BY—protein125——
Ba—protein97——
Bb—protein80——
Be—protein55——
A3—rna157——
A4—rna119——
AA—protein252——
AB—protein394——
AC—protein363——
AD—protein294——
AE—protein194——
AF—protein234——
AG—protein234——
AH—protein191——
AI—protein208——
AJ—protein169——
AL—protein205——
AM—protein139——
AN—protein203——
AO—protein195——
AP—protein153——
AQ—protein187——
AR—protein181——
AS—protein175——
AT—protein157——
AU—protein99——
AV—protein129——
AW—protein121——
AX—protein117——
AY—protein127——
AZ—protein134——
Aa—protein147——
Ab—protein68——
Ac—protein103——
Ad—protein106——
Ae—protein129——
Af—protein109——
Ag—protein114——
Ah—protein122——
Ai—protein97——
Aj—protein84——
Ak—protein69——
Al—protein50——
Am—protein50——
An—protein25——
Ao—protein105——
Ap—protein91——
At—protein122——
Au—protein217——
Aq—protein151——
AK—protein202——
Ct—protein853——

Ligands and binding sites

  • GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A2, Ct
  • MG · Magnesium ion · metal · 327 copies · chains A2, Aa, AN, AP, AD, AC, AO, Ai, AL, AA, AQ, Ab, A3, A4, AF, AB, Ae, Bx, B1, Ct, BX, BD, Ba, AY, An
  • ZN · Zinc ion · metal · 5 copies · chains Bd, Ba, Aj, Ao, Ap

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

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