Research workbench

E. coli Microcin synthetase McbBCD complex with truncated pro-MccB17 bound

Analyse E. coli Microcin synthetase McbBCD complex with truncated pro-MccB17 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GRH
Type: protein
Length: 1,250 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.85
Source: Escherichia coli str. K-12 substr. MG1655
Molecule: Bacteriocin microcin B17; Microcin B17-processing protein McbB; Microcin B17-processing…
UniProt: P05834, P23184, P23185, P23186
Ligands: FMN, ZN, CL, SO4
Pockets: 18 · best druggability 0.83

Structure

x-ray diffraction · resolution 1.85 · 4 distinct chains · 36% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bacteriocin microcin B17	protein	20	25% helix, 35% strand	P05834
1, 2	Microcin B17-processing protein McbB	protein	284	33% helix, 24% strand	P23184
C	Microcin B17-processing protein McbC	protein	266	37% helix, 18% strand	P23185
D	Microcin B17-processing protein McbD	protein	396	37% helix, 21% strand	P23186

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · chains C
ZN · Zinc ion · metal · 2 copies · chains 1, 2
CL · Chloride ion · ion · 2 copies · chains 1, D
SO4 · Sulfate ion · ion · chains 1
EDO · 1,2-ethanediol · additive · 7 copies · chains 1, 2, D, C
GOL · Glycerol · additive · chains D

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

Pockets

18 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	1091	0.83	0.84	85	GOL
2	953	0.78	0.80	66	empty
3	1130	0.73	0.76	108	EDO
4	51	0.70	0.98	23	empty
5	114	0.62	0.88	28	EDO

Interfaces

7 interfaces between chains.

2–D · 2315 Å² buried · 52 hydrogen bonds · protein-protein
1–2 · 1618 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1046 Å² buried · 23 hydrogen bonds · protein-protein
A–1 · 663 Å² buried · 9 hydrogen bonds · protein-protein
A–2 · 340 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6GRH · E. COLI microcin synthetase mcbbcd complex with truncated pro-MCCB17 bound · the same entry in another collection · chain D against D, TM-score 1.00
P23186 · AlphaFold monomer V2.0 prediction for microcin B17-processing protein mcbd (P23186) · a predicted model of the same protein · chain D against A, TM-score 1.00
P23185 · AlphaFold monomer V2.0 prediction for microcin B17-processing protein mcbc (P23185) · a predicted model of the same protein · chain C against A, TM-score 0.94
P23184 · AlphaFold monomer V2.0 prediction for microcin B17-processing protein mcbb (P23184) · a predicted model of the same protein · chain 1 against A, TM-score 0.89
P05834 · AlphaFold monomer V2.0 prediction for bacteriocin microcin B17 (P05834) · a predicted model of the same protein · chain A against A, TM-score 0.59

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 P05834
Every structure of UniProt P23184
Every structure of UniProt P23185
Every structure of UniProt P23186
Elsewhere: RCSB PDB 6GRH · PDBe 6GRH · UniProt P05834 · UniProt P23184 · UniProt P23185 · UniProt P23186

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