MolNFT v1 · #23224 · protein + RNA

Phe-tRNA, elongation factor ef-TU:GDPNP ternary complex

1TTT · Transfer ribonucleic acid (yeast, phe): “Phe-tRNA, elongation factor ef-TU:GDPNP ternary complex”. X-ray diffraction, 3 ligands (PHE, GNP, MG), 20 pockets (best druggability 0.80). MolNFT v1 #23224 on GenesisL1: 3D structure…

PDB: 1TTT
Type: protein + RNA
Length: 1,443 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transfer ribonucleic acid (yeast, phe); Of elongation factor tu (ef-tu)
UniProt: Q01698
Ligands: PHE, GNP, MG
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, E, F	Transfer ribonucleic acid (yeast, phe)	rna	76	—	—
A, B, C	Of elongation factor tu (ef-tu)	protein	405	24% helix, 35% strand	Q01698

Ligands and binding sites

PHE · Phenylalanine · ligand · 3 copies · chains D, A, E, B, F, C
GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 3 copies · chains A, B, C
MG · Magnesium ion · metal · 6 copies · chains D, E, F, A, B, C

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	940	0.80	0.83	79	MG
2	848	0.80	0.83	78	PHE
3	632	0.79	0.85	60	MG
4	340	0.78	0.89	47	PHE
5	363	0.72	0.85	33	MG

Interfaces

9 interfaces between chains.

E–B · 1414 Å² buried · 33 hydrogen bonds · protein-nucleic
F–C · 1402 Å² buried · 31 hydrogen bonds · protein-nucleic
D–A · 1380 Å² buried · 32 hydrogen bonds · protein-nucleic
E–C · 379 Å² buried · 4 hydrogen bonds · protein-nucleic
D–F · 364 Å² buried · 11 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 42 modified, 3 covalent (nucleotide modification, covalent ligand).

Compared structures

1TTT · Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex · the same entry in another collection · chain C against C, TM-score 1.00
Q01698 · AlphaFold monomer V2.0 prediction for elongation factor tu (Q01698) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q01698
Elsewhere: RCSB PDB 1TTT · PDBe 1TTT · UniProt Q01698

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