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Crystal structure of probable alanyl-tRNA-synthase from clostridium perfringens

Analyse Crystal structure of probable alanyl-tRNA-synthase from clostridium perfringens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KEW
Type: protein
Length: 458 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DHHA1 domain protein
UniProt: Q0TT74
Ligands: ZN
Pockets: 6 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DHHA1 domain protein	protein	230	23% helix, 39% strand	Q0TT74
B	DHHA1 domain protein	protein	228	25% helix, 39% strand	Q0TT74

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

6 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	55	0.57	0.91	18	empty
2	186	0.55	0.80	30	ZN
3	204	0.54	0.78	30	ZN
4	173	0.44	0.74	23	empty
5	66	0.36	0.78	13	empty

Interfaces

1 interface between chains.

A–B · 337 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

3KEW · Crystal structure of probable alanyl-trna-synthase from Clostridium perfringens · the same entry in another collection · chain A against A, TM-score 1.00

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 Q0TT74
Elsewhere: RCSB PDB 3KEW · PDBe 3KEW · UniProt Q0TT74

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