MolNFT v1 · #117386 · protein + RNA

Crystal structure of human wild type glyrs bound with trnagly

5E6M · Glycine--tRNA ligase: “Crystal structure of human wild type glyrs bound with trnagly”. X-ray diffraction, 3 ligands (GAP, NI, SO4), 20 pockets (best druggability 0.83). MolNFT v1 #117386 on GenesisL1: 3D structure, binding sites and…

PDB: 5E6M
Type: protein + RNA
Length: 1,173 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycine--tRNA ligase; TRNA(GLY)
EC: 6.1.1.14
UniProt: P41250
Ligands: GAP, NI, SO4
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycine--tRNA ligase (EC 6.1.1.14)	protein	519	39% helix, 24% strand	P41250
B	Glycine--tRNA ligase (EC 6.1.1.14)	protein	506	34% helix, 28% strand	P41250
C, E	TRNA(GLY)	rna	74	—	—

Ligands and binding sites

GAP · Glycyl-adenosine-5'-phosphate · ligand · 2 copies · chains A, E, B, C
NI · Nickel (II) ion · metal · 2 copies · chains C, E
SO4 · Sulfate ion · ion · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	467	0.83	0.90	58	empty
2	1090	0.82	0.83	77	NI
3	263	0.81	0.93	34	empty
4	999	0.80	0.82	90	GAP, SO4
5	823	0.76	0.80	73	GAP

Interfaces

5 interfaces between chains.

A–B · 3340 Å² buried · 37 hydrogen bonds · protein-protein
B–C · 1942 Å² buried · 52 hydrogen bonds · protein-nucleic
A–E · 1878 Å² buried · 52 hydrogen bonds · protein-nucleic
B–E · 602 Å² buried · 12 hydrogen bonds · protein-nucleic
A–C · 587 Å² buried · 9 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

5E6M · Crystal structure of human wild type GlyRS bound with tRNAGly · the same entry in another collection · chain A against A, TM-score 1.00
P41250 · AlphaFold monomer V2.0 prediction for glycine--tRNA ligase (P41250) · 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 P41250
Elsewhere: RCSB PDB 5E6M · PDBe 5E6M · UniProt P41250

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