MolNFT v1 · #168505 · protein

Cdib from escherichia COLI

6WIM · Outer membrane transporter cdib: “Cdib from escherichia COLI”. X-ray diffraction, 5 pockets (best druggability 0.87). MolNFT v1 #168505 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6WIM
Type: protein
Length: 536 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Outer membrane transporter cdib
UniProt: Q3YL97
Pockets: 5 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Outer membrane transporter cdib	protein	536	15% helix, 49% strand	Q3YL97

Ligands and binding sites

PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains A
EDO · 1,2-ethanediol · additive · 5 copies · chains A

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

Pockets

5 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	942	0.87	0.89	108	empty
2	445	0.63	0.77	55	empty
3	198	0.63	0.83	29	empty
4	95	0.47	0.81	20	empty
5	57	0.28	0.75	15	empty

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6WIM · CdiB from Escherichia coli · the same entry in another collection · chain A against A, TM-score 1.00
Q3YL97 · AlphaFold monomer V2.0 prediction for outer membrane transporter cdib (Q3YL97) · 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 Q3YL97
Elsewhere: RCSB PDB 6WIM · PDBe 6WIM · UniProt Q3YL97

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