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Ion selectivity of ompf porin soaked in 0.3M kbr

Analyse Ion selectivity of ompf porin soaked in 0.3M kbr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4LSI
Type: protein
Length: 1,002 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Outer membrane protein F
UniProt: P02931
Ligands: MG, BR
Pockets: 11 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 58% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Outer membrane protein F	protein	334	4% helix, 58% strand	P02931

Ligands and binding sites

MG · Magnesium ion · metal · 8 copies · chains A, B, C
BR · Bromide ion · ion · 9 copies · chains A, B, C
PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A, C, B
C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 4 copies · chains A, B, C
GOL · Glycerol · additive · 4 copies · chains A, B, C

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

Pockets

11 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	1063	0.71	0.75	70	PEG, GOL, BR
2	1047	0.70	0.75	66	PEG, GOL, BR
3	973	0.70	0.75	62	PEG, GOL, BR
4	254	0.48	0.74	38	empty
5	232	0.47	0.73	35	empty

Interfaces

3 interfaces between chains.

B–C · 1450 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 1349 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1330 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

4LSI · Ion selectivity of OmpF porin soaked in 0.3M KBr · the same entry in another collection · chain A against A, TM-score 1.00
P02931 · AlphaFold monomer V2.0 prediction for outer membrane porin F (P02931) · a predicted model of the same protein · 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 P02931
Elsewhere: RCSB PDB 4LSI · PDBe 4LSI · UniProt P02931

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