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Crystal structure of the initiation module of lgra in the thiolation state

Analyse Crystal structure of the initiation module of lgra in the thiolation state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ES8
Type: protein
Length: 1,527 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Linear gramicidin synthetase subunit a
UniProt: Q70LM7
Ligands: 5S4
Pockets: 13 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Linear gramicidin synthetase subunit a	protein	759	33% helix, 22% strand	Q70LM7
B	Linear gramicidin synthetase subunit a	protein	768	33% helix, 22% strand	Q70LM7

Ligands and binding sites

5S4 · [(3~{R})-4-[[3-[2-[[(2~{S})-2-azanyl-3-methyl-butanoyl]amino]ethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate · ligand · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	850	0.83	0.85	98	5S4
2	924	0.82	0.83	112	5S4
3	696	0.74	0.80	70	empty
4	541	0.73	0.81	56	empty
5	259	0.63	0.81	42	empty

Interfaces

1 interface between chains.

A–B · 885 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

5ES8 · Crystal structure of the initiation module of LgrA in the thiolation state · the same entry in another collection · chain A against A, TM-score 1.00
Q70LM7 · AlphaFold monomer V2.0 prediction for linear gramicidin synthase subunit a (Q70LM7) · a predicted model of the same protein · chain A against A, TM-score 0.79

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 Q70LM7
Elsewhere: RCSB PDB 5ES8 · PDBe 5ES8 · UniProt Q70LM7

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