Research workbench

Crystal structure of a native bcse (349-523) rq complex with C-di-gmp and ATP bound

Analyse Crystal structure of a native bcse (349-523) rq complex with C-di-gmp and ATP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YBU
Type: protein
Length: 1,742 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bacterial cellulose secretion regulator bcsq; Bacterial cellulose secretion regulator…
UniProt: A0A0B1KWQ0, J7QAC9, P37657
Ligands: C2E, ATP, MG
Pockets: 10 · best druggability 0.89

Structure

x-ray diffraction · 9 distinct chains · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, G	Bacterial cellulose secretion regulator bcsq	protein	240	45% helix, 16% strand	A0A0B1KWQ0
C	Bacterial cellulose secretion regulator bcsr	protein	29	52% helix, 3% strand	J7QAC9
D	Bacterial cellulose secretion regulator bcsr	protein	29	66% helix, 3% strand	J7QAC9
E	Bacterial cellulose secretion regulator bcse, residues 349- 523	protein	168	38% helix, 22% strand	P37657
F, K	Bacterial cellulose secretion regulator bcse, residues 349- 523	protein	166	37% helix, 23% strand	P37657
H	Bacterial cellulose secretion regulator bcsq	protein	239	44% helix, 20% strand	A0A0B1KWQ0
I	Bacterial cellulose secretion regulator bcsr	protein	30	60% helix, 3% strand	J7QAC9
J	Bacterial cellulose secretion regulator bcsr	protein	33	48% helix, 9% strand	J7QAC9
L	Bacterial cellulose secretion regulator bcse, residues 349- 523	protein	162	37% helix, 24% 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 · 8 copies · chains E, F, K, L
ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, G, H
MG · Magnesium ion · metal · 4 copies · chains A, B, G, H

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

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	960	0.89	0.91	112	ATP, MG
2	668	0.88	0.92	106	ATP, MG
3	97	0.68	0.92	22	empty
4	416	0.64	0.78	50	empty
5	476	0.63	0.76	62	empty

Interfaces

21 interfaces between chains.

A–B · 1588 Å² buried · 25 hydrogen bonds · protein-protein
G–H · 1558 Å² buried · 19 hydrogen bonds · protein-protein
G–K · 1532 Å² buried · 32 hydrogen bonds · protein-protein
H–L · 1474 Å² buried · 29 hydrogen bonds · protein-protein
B–F · 1444 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

6YBU · Crystal structure of a native BcsE (349-523) RQ complex with c-di-GMP and ATP bound · the same entry in another collection · chain L against L, TM-score 1.00

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 6YBU · PDBe 6YBU · UniProt A0A0B1KWQ0 · UniProt J7QAC9 · UniProt P37657

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.