Research workbench

Recombinant thiocyanate hydrolase, fully-matured form

Analyse Recombinant thiocyanate hydrolase, fully-matured form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2DXC
Type: protein
Length: 1,955 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thiocyanate hydrolase subunit alpha; Thiocyanate hydrolase subunit beta; Thiocyanate…
EC: 3.5.5.8
UniProt: O66187, O66186, O66188
Ligands: 3CO
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 7 distinct chains · 44% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Thiocyanate hydrolase subunit alpha (EC 3.5.5.8)	protein	119	22% helix, 29% strand	O66187
B, K	Thiocyanate hydrolase subunit beta (EC 3.5.5.8)	protein	152	62% helix, 7% strand	O66186
C, I	Thiocyanate hydrolase subunit gamma (EC 3.5.5.8)	protein	217	41% helix, 13% strand	O66188
E	Thiocyanate hydrolase subunit beta (EC 3.5.5.8)	protein	151	59% helix, 6% strand	O66186
F, L	Thiocyanate hydrolase subunit gamma (EC 3.5.5.8)	protein	216	40% helix, 13% strand	O66188
G, J	Thiocyanate hydrolase subunit alpha (EC 3.5.5.8)	protein	120	21% helix, 28% strand	O66187
H	Thiocyanate hydrolase subunit beta (EC 3.5.5.8)	protein	156	59% helix, 6% strand	O66186

Ligands and binding sites

3CO · Cobalt (III) ion · metal · 4 copies · chains C, F, I, L
TLA · L(+)-tartaric acid · additive · 4 copies · chains B, C, E, F, H, I, 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, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	672	0.88	0.93	82	empty
2	857	0.87	0.90	95	empty
3	1186	0.83	0.84	170	empty
4	906	0.81	0.83	124	empty
5	53	0.69	0.97	23	empty

Interfaces

46 interfaces between chains.

H–I · 3405 Å² buried · 52 hydrogen bonds · protein-protein
B–C · 3397 Å² buried · 54 hydrogen bonds · protein-protein
K–L · 3391 Å² buried · 51 hydrogen bonds · protein-protein
E–F · 3352 Å² buried · 51 hydrogen bonds · protein-protein
A–C · 1624 Å² buried · 46 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (oxidation).

Compared structures

2DXC · Recombinant thiocyanate hydrolase, fully-matured form · 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 O66187
Every structure of UniProt O66186
Every structure of UniProt O66188
Elsewhere: RCSB PDB 2DXC · PDBe 2DXC · UniProt O66187 · UniProt O66186 · UniProt O66188

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