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E. COLI fold in complex with carolacton

Analyse E. COLI fold in complex with carolacton in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5O22
Type: protein
Length: 1,117 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bifunctional protein fold
EC: 1.5.1.5, 3.5.4.9
UniProt: P24186
Ligands: C3R
Pockets: 13 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bifunctional protein fold (EC 1.5.1.5, 3.5.4.9)	protein	280	43% helix, 16% strand	P24186
B	Bifunctional protein fold (EC 1.5.1.5, 3.5.4.9)	protein	280	43% helix, 16% strand	P24186
C	Bifunctional protein fold (EC 1.5.1.5, 3.5.4.9)	protein	284	44% helix, 16% strand	P24186
D	Bifunctional protein fold (EC 1.5.1.5, 3.5.4.9)	protein	273	44% helix, 15% strand	P24186

Ligands and binding sites

C3R · Carolacton · ligand · 4 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	881	0.74	0.78	97	empty
2	520	0.65	0.76	56	C3R
3	426	0.63	0.77	48	C3R
4	488	0.61	0.75	43	C3R
5	411	0.59	0.75	47	C3R

Interfaces

5 interfaces between chains.

A–B · 1687 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 1493 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 216 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 158 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 13 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (methylation).

Compared structures

5O22 · E. coli FolD in complex with carolacton · the same entry in another collection · chain D against D, TM-score 1.00
P24186 · AlphaFold monomer V2.0 prediction for bifunctional protein fold (P24186) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P24186
Elsewhere: RCSB PDB 5O22 · PDBe 5O22 · UniProt P24186

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