MolNFT v1 · #40734 · protein

Osmoporin ompc

2J1N · Outer membrane protein C: “Osmoporin ompc”. X-ray diffraction, 3 ligands (D12, MG, CL), 9 pockets (best druggability 0.79). MolNFT v1 #40734 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2J1N
Type: protein
Length: 1,038 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Outer membrane protein C
UniProt: P06996
Ligands: D12, MG, CL
Pockets: 9 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Outer membrane protein C	protein	346	6% helix, 56% strand	P06996

Ligands and binding sites

D12 · Dodecane · ligand · 11 copies · chains C
MG · Magnesium ion · metal · 3 copies · chains A, B, C
CL · Chloride ion · ion · 2 copies · chains B, A, C

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	115	0.79	0.97	32	empty
2	1057	0.73	0.77	98	empty
3	866	0.73	0.77	63	empty
4	1183	0.71	0.75	77	empty
5	296	0.51	0.74	41	D12

Interfaces

3 interfaces between chains.

A–B · 1625 Å² buried · 32 hydrogen bonds · protein-protein
A–C · 1615 Å² buried · 31 hydrogen bonds · protein-protein
B–C · 1613 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

2J1N · osmoporin OmpC · the same entry in another collection · chain A against A, TM-score 1.00
P06996 · AlphaFold monomer V2.0 prediction for outer membrane porin C (P06996) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P06996
Elsewhere: RCSB PDB 2J1N · PDBe 2J1N · UniProt P06996

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