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E. COLI microcin synthetase mcbbcd complex with pro-MCCB17, ADP and phosphate bound

Analyse E. COLI microcin synthetase mcbbcd complex with pro-MCCB17, ADP and phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GRG
Type: protein
Length: 1,247 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bacteriocin microcin B17; Microcin B17-processing protein mcbb; Microcin B17-processing…
UniProt: P05834, P23184, P23185, P23186
Ligands: F6N, FMN, ATP, ADP, MG, ZN, SO4, PO4, CL
Pockets: 14 · best druggability 0.87

Structure

x-ray diffraction · 5 distinct chains · 35% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bacteriocin microcin B17	protein	20	25% helix, 35% strand	P05834
1	Microcin B17-processing protein mcbb	protein	284	32% helix, 24% strand	P23184
2	Microcin B17-processing protein mcbb	protein	282	35% helix, 22% strand	P23184
C	Microcin B17-processing protein mcbc	protein	265	35% helix, 18% strand	P23185
D	Microcin B17-processing protein mcbd	protein	396	37% helix, 22% strand	P23186

Ligands and binding sites

F6N · 2-(aminomethyl)-1,3-oxazole-4-carboxylic acid · ligand · chains A, C
FMN · Flavin mononucleotide · ligand · chains A, C
ATP · Adenosine-5'-triphosphate · ligand · chains 2
ADP · Adenosine-5'-diphosphate · ligand · chains D
MG · Magnesium ion · metal · 3 copies · chains D
ZN · Zinc ion · metal · 2 copies · chains 1, 2
SO4 · Sulfate ion · ion · chains 1
PO4 · Phosphate ion · ion · chains D
CL · Chloride ion · ion · chains D
EDO · 1,2-ethanediol · additive · 2 copies · chains 2, D
GOL · Glycerol · additive · chains 1

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1094	0.87	0.88	126	ADP, PO4, MG
2	1129	0.73	0.76	109	EDO
3	53	0.70	0.98	22	empty
4	123	0.62	0.87	28	empty
5	146	0.47	0.76	18	empty

Interfaces

8 interfaces between chains.

2–D · 2330 Å² buried · 53 hydrogen bonds · protein-protein
1–2 · 1602 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 1016 Å² buried · 22 hydrogen bonds · protein-protein
A–1 · 629 Å² buried · 8 hydrogen bonds · protein-protein
A–2 · 346 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

6GRG · E. coli Microcin synthetase McbBCD complex with pro-MccB17, ADP and phosphate 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 6GRG · PDBe 6GRG · UniProt P05834 · UniProt P23184 · UniProt P23185 · UniProt P23186

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