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Crystal structure of cyanase from the thermophilic fungus thermomyces lanuginosus

Analyse Crystal structure of cyanase from the thermophilic fungus thermomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XGT
Type: protein
Length: 1,592 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyanate hydratase
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, F, G, H, B, A, I, J	Cyanate hydratase	protein	159	45% helix, 18% strand	—
D, C	Cyanate hydratase	protein	160	44% helix, 18% strand	—

Ligands and binding sites

FMT · Formic acid · additive · 4 copies · chains E, F, I, J, B, C
MLI · Malonate ion · additive · 3 copies · chains E, F, G, H, A, D, B, C

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

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	975	0.77	0.79	116	empty
2	797	0.74	0.79	93	empty
3	155	0.66	0.87	35	empty
4	137	0.66	0.88	34	empty
5	122	0.65	0.88	31	empty

Interfaces

25 interfaces between chains.

B–C · 3723 Å² buried · 34 hydrogen bonds · protein-protein
I–J · 3697 Å² buried · 36 hydrogen bonds · protein-protein
A–D · 3689 Å² buried · 36 hydrogen bonds · protein-protein
G–H · 3681 Å² buried · 39 hydrogen bonds · protein-protein
E–F · 3678 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

6XGT · Crystal structure of cyanase from the thermophilic fungus Thermomyces lanuginosus · the same entry in another collection · chain I against I, 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
Elsewhere: RCSB PDB 6XGT · PDBe 6XGT

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