MolNFT v1 · #150369 · protein

E. COLI microcin synthetase mcbbcd complex

6GRI · Microcin B17-processing protein mcbb: “E. COLI microcin synthetase mcbbcd complex”. X-ray diffraction, 4 ligands (FMN, ZN, CL), 18 pockets (best druggability 0.85). MolNFT v1 #150369 on GenesisL1: 3D structure, binding sites and…

PDB: 6GRI
Type: protein
Length: 1,207 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Microcin B17-processing protein mcbb; Microcin B17-processing protein mcbc; Microcin…
UniProt: P23184, P23185, P23186
Ligands: FMN, ZN, CL, SO4
Pockets: 18 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Microcin B17-processing protein mcbb	protein	284	31% helix, 23% strand	P23184
2	Microcin B17-processing protein mcbb	protein	264	36% helix, 25% strand	P23184
C	Microcin B17-processing protein mcbc	protein	266	39% helix, 19% strand	P23185
D	Microcin B17-processing protein mcbd	protein	393	36% helix, 22% 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 · 3 copies · chains 1, C, D
SO4 · Sulfate ion · ion · 2 copies · chains 1, C

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	926	0.85	0.87	109	empty
2	57	0.72	0.99	20	empty
3	438	0.61	0.76	55	empty
4	129	0.60	0.85	31	empty
5	425	0.58	0.75	62	empty

Interfaces

4 interfaces between chains.

2–D · 1806 Å² buried · 28 hydrogen bonds · protein-protein
1–2 · 1542 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1039 Å² buried · 19 hydrogen bonds · protein-protein
1–C · 112 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6GRI · E. coli Microcin synthetase McbBCD complex · 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

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

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