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Colicin E1 fragment in nanodisc-embedded tolc

Analyse Colicin E1 fragment in nanodisc-embedded tolc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WXI
Type: protein
Length: 1,284 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Outer membrane protein tolc
UniProt: P02930
Pockets: 17 · best druggability 0.70

Structure

electron microscopy · 1 distinct chain · 67% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Outer membrane protein tolc	protein	428	67% helix, 16% strand	P02930

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	739	0.70	0.77	104	empty
2	157	0.44	0.75	25	empty
3	107	0.42	0.77	16	empty
4	90	0.40	0.77	21	empty
5	94	0.40	0.77	16	empty

Interfaces

3 interfaces between chains.

B–C · 2495 Å² buried · 50 hydrogen bonds · protein-protein
A–B · 2491 Å² buried · 50 hydrogen bonds · protein-protein
A–C · 2489 Å² buried · 50 hydrogen bonds · protein-protein

Compared structures

6WXI · Colicin E1 fragment in nanodisc-embedded TolC · the same entry in another collection · chain A against A, TM-score 1.00
P02930 · AlphaFold monomer V2.0 prediction for outer membrane protein tolc (P02930) · 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 P02930
Elsewhere: RCSB PDB 6WXI · PDBe 6WXI · UniProt P02930

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