Research workbench

Outer membrane protein ompw

Analyse Outer membrane protein ompw in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2F1V
Type: protein
Length: 1,092 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Outer membrane protein W
UniProt: P0A915
Pockets: 15 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 69% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Outer membrane protein W	protein	182	3% helix, 69% strand	P0A915

Ligands and binding sites

GOL · Glycerol · additive · 6 copies · chains A, F, E, C, D, B

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

Pockets

15 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	1076	0.86	0.87	86	empty
2	1178	0.86	0.86	93	empty
3	863	0.79	0.83	86	empty
4	835	0.79	0.83	90	empty
5	101	0.50	0.81	20	empty

Interfaces

9 interfaces between chains.

B–C · 734 Å² buried · 2 hydrogen bonds · protein-protein
C–E · 682 Å² buried · 13 hydrogen bonds · protein-protein
A–F · 681 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 672 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 670 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

2F1V · Outer membrane protein OmpW · the same entry in another collection · chain C against C, TM-score 1.00
P0A915 · AlphaFold monomer V2.0 prediction for outer membrane protein W (P0A915) · 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 P0A915
Elsewhere: RCSB PDB 2F1V · PDBe 2F1V · UniProt P0A915

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