Research workbench

Crystal structure of putative amidohydrolase BH0493 from bacillus halodurans C-125

Analyse Crystal structure of putative amidohydrolase BH0493 from bacillus halodurans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QEE
Type: protein
Length: 4,995 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BH0493 protein
UniProt: Q9KFI6
Ligands: ZN, MG, CL
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 7 distinct chains · 57% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, G	BH0493 protein	protein	415	57% helix, 9% strand	Q9KFI6
C	BH0493 protein	protein	417	57% helix, 9% strand	Q9KFI6
E	BH0493 protein	protein	424	56% helix, 9% strand	Q9KFI6
F, H, I	BH0493 protein	protein	416	57% helix, 9% strand	Q9KFI6
J	BH0493 protein	protein	414	57% helix, 9% strand	Q9KFI6
K	BH0493 protein	protein	414	58% helix, 9% strand	Q9KFI6
L	BH0493 protein	protein	418	57% helix, 9% strand	Q9KFI6

Ligands and binding sites

ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
MG · Magnesium ion · metal · 4 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
CL · Chloride ion · ion · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	849	0.77	0.80	86	empty
2	439	0.70	0.81	47	empty
3	739	0.67	0.75	66	empty
4	329	0.66	0.81	38	empty
5	391	0.65	0.79	46	empty

Interfaces

22 interfaces between chains.

D–E · 2084 Å² buried · 39 hydrogen bonds · protein-protein
G–H · 2081 Å² buried · 38 hydrogen bonds · protein-protein
J–L · 2079 Å² buried · 39 hydrogen bonds · protein-protein
G–I · 2078 Å² buried · 39 hydrogen bonds · protein-protein
K–L · 2076 Å² buried · 40 hydrogen bonds · protein-protein

Compared structures

2QEE · Crystal structure of putative amidohydrolase BH0493 from Bacillus halodurans C-125 · the same entry in another collection · chain A against A, 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 Q9KFI6
Elsewhere: RCSB PDB 2QEE · PDBe 2QEE · UniProt Q9KFI6

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