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The structure of ompf porin in a tetragonal crystal form

Analyse The structure of ompf porin in a tetragonal crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1OPF
Type: protein
Length: 2,040 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Matrix porin outer membrane protein F
UniProt: P02931
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 61% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Matrix porin outer membrane protein F	protein	340	5% helix, 61% strand	P02931

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	862	0.72	0.77	79	empty
2	974	0.71	0.75	71	empty
3	1010	0.71	0.75	74	empty
4	942	0.70	0.75	63	empty
5	957	0.70	0.75	61	empty

Interfaces

9 interfaces between chains.

E–F · 1499 Å² buried · 22 hydrogen bonds · protein-protein
D–F · 1498 Å² buried · 22 hydrogen bonds · protein-protein
D–E · 1498 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 1498 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 1494 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

1OPF · The structure of ompf porin in a tetragonal crystal form · the same entry in another collection · chain C against C, 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 1OPF · PDBe 1OPF · UniProt P02931

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