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Crystal structure of a native bcse (217-523) - bcsr-bcsq (R156E mutant) complex with C-di-gmp and ATP bound

Analyse Crystal structure of a native bcse (217-523) - bcsr-bcsq (R156E mutant) complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YBB
Type: protein
Length: 1,118 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bacterial cellulose secretion regulator bcsq, R156E mutant; Bacterial cellulose secretion…
UniProt: A0A0B1KWQ0, J7QAC9, P37657
Ligands: C2E, ATP, MG
Pockets: 10 · best druggability 0.89

Structure

x-ray diffraction · 5 distinct chains · 40% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Bacterial cellulose secretion regulator bcsq, R156E mutant	protein	243	45% helix, 17% strand	A0A0B1KWQ0
C	Bacterial cellulose secretion regulator bcsr	protein	22	82% helix, 0% strand	J7QAC9
D	Bacterial cellulose secretion regulator bcsr	protein	51	27% helix, 20% strand	J7QAC9
E	Bacterial cellulose secretion regulator bcse, residues 217- 523	protein	279	38% helix, 20% strand	P37657
F	Bacterial cellulose secretion regulator bcse, residues 217- 523	protein	280	36% helix, 20% strand	P37657

Ligands and binding sites

C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 4 copies · chains E, F
ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains E, F

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

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1065	0.89	0.91	110	MG, ATP
2	299	0.59	0.78	40	C2E
3	169	0.51	0.78	23	empty
4	114	0.49	0.80	17	empty
5	54	0.49	0.86	20	empty

Interfaces

9 interfaces between chains.

A–B · 1514 Å² buried · 18 hydrogen bonds · protein-protein
B–F · 1374 Å² buried · 20 hydrogen bonds · protein-protein
A–E · 1355 Å² buried · 20 hydrogen bonds · protein-protein
B–D · 548 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 464 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6YBB · Crystal structure of a native BcsE (217-523) - BcsR-BcsQ (R156E mutant) complex with… · the same entry in another collection · chain F against F, TM-score 1.00
P37657 · AlphaFold monomer V2.0 prediction for cyclic di-gmp binding protein bcse (P37657) · a predicted model of the same protein · chain E against A, TM-score 0.92

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 A0A0B1KWQ0
Every structure of UniProt J7QAC9
Every structure of UniProt P37657
Elsewhere: RCSB PDB 6YBB · PDBe 6YBB · UniProt A0A0B1KWQ0 · UniProt J7QAC9 · UniProt P37657

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