MolNFT v1 · #56639 · protein

Structure of ompf co-crystallized with T83

2ZLD · Outer membrane protein F: “Structure of ompf co-crystallized with T83”. X-ray diffraction, 4 pockets (best druggability 0.76). MolNFT v1 #56639 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2ZLD
Type: protein
Length: 692 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Outer membrane protein F; Colicin-E3
EC: 3.1.-.-
UniProt: P02931
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 58% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Outer membrane protein F	protein	339	4% helix, 59% strand	P02931
C, D	Colicin-E3 (EC 3.1.-.-)	protein	7	0% helix, 0% strand	—

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1124	0.76	0.79	100	empty
2	1038	0.76	0.79	110	empty
3	184	0.45	0.74	30	empty
4	64	0.44	0.81	13	empty

Interfaces

3 interfaces between chains.

A–B · 617 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 255 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 230 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

2ZLD · Structure of OmpF co-crystallized with T83 · 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 2ZLD · PDBe 2ZLD · UniProt P02931

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