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Crystal structure of seryl-tRNA synthetase from pyrococcus horikoshii

Analyse Crystal structure of seryl-tRNA synthetase from pyrococcus horikoshii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2ZR3
Type: protein
Length: 896 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Seryl-tRNA synthetase
EC: 6.1.1.11
UniProt: O58441
Pockets: 8 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Seryl-tRNA synthetase (EC 6.1.1.11)	protein	448	43% helix, 23% strand	O58441

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	750	0.74	0.79	62	empty
2	690	0.73	0.80	57	empty
3	152	0.73	0.91	30	empty
4	79	0.36	0.76	15	empty
5	81	0.34	0.75	16	empty

Interfaces

1 interface between chains.

A–B · 2429 Å² buried · 48 hydrogen bonds · protein-protein

Compared structures

2ZR3 · Crystal structure of seryl-tRNA synthetase from Pyrococcus horikoshii · the same entry in another collection · chain A against A, TM-score 1.00
O58441 · AlphaFold monomer V2.0 prediction for serine--tRNA ligase (O58441) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 O58441
Elsewhere: RCSB PDB 2ZR3 · PDBe 2ZR3 · UniProt O58441

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