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Crystal structure of an L-amino acid ligase riza

Analyse Crystal structure of an L-amino acid ligase riza in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4WD3
Type: protein
Length: 776 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-amino acid ligase
UniProt: B5UAT8
Pockets: 8 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	L-amino acid ligase	protein	388	36% helix, 28% strand	B5UAT8

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1144	0.77	0.79	135	empty
2	404	0.71	0.83	50	empty
3	298	0.62	0.79	48	empty
4	206	0.54	0.78	31	empty
5	107	0.40	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 1330 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 modified (engineered).

Compared structures

4WD3 · Crystal structure of an L-amino acid ligase RizA · the same entry in another collection · chain A against A, TM-score 1.00
B5UAT8 · AlphaFold monomer V2.0 prediction for L-arginine-specific L-amino acid ligase (B5UAT8) · 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 B5UAT8
Elsewhere: RCSB PDB 4WD3 · PDBe 4WD3 · UniProt B5UAT8

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