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Crystal structure of the lgra initiation module excluding the asub domain: F-a-delta-sub

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

PDB: 5JNF
Type: protein
Length: 2,329 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Linear gramicidin synthase subunit a
UniProt: Q70LM7
Pockets: 19 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 31% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Linear gramicidin synthase subunit a	protein	583	32% helix, 25% strand	Q70LM7
A	Linear gramicidin synthase subunit a	protein	585	31% helix, 25% strand	Q70LM7
B	Linear gramicidin synthase subunit a	protein	580	30% helix, 24% strand	Q70LM7
D	Linear gramicidin synthase subunit a	protein	581	32% helix, 25% strand	Q70LM7

Ligands and binding sites

FMT · Formic acid · additive · 5 copies · chains C, A

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

Pockets

19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	843	0.78	0.81	82	FMT
2	868	0.77	0.80	74	FMT
3	549	0.70	0.80	58	empty
4	527	0.70	0.80	62	empty
5	286	0.68	0.83	39	empty

Interfaces

2 interfaces between chains.

C–A · 1790 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 243 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5JNF · Crystal structure of the LgrA initiation module excluding the Asub domain: F-A-delta-sub · the same entry in another collection · chain D against D, 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 0.98

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 5JNF · PDBe 5JNF · UniProt Q70LM7

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