MolNFT v1 · #144378 · protein

The crystal structure of isothiocyanate hydrolase from delia radicum gut bacteria

6BRM · Putative metal-dependent isothiocyanate hydrolase saxa: “The crystal structure of isothiocyanate hydrolase from delia radicum gut bacteria”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.66). MolNFT v1 #144378 on…

PDB: 6BRM
Type: protein
Length: 2,087 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative metal-dependent isothiocyanate hydrolase saxa
UniProt: A0A0N7FW12
Ligands: ZN
Pockets: 20 · best druggability 0.66

Structure

x-ray diffraction · 5 distinct chains · 23% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Putative metal-dependent isothiocyanate hydrolase saxa	protein	262	23% helix, 26% strand	A0A0N7FW12
B	Putative metal-dependent isothiocyanate hydrolase saxa	protein	263	24% helix, 25% strand	A0A0N7FW12
D, E, G	Putative metal-dependent isothiocyanate hydrolase saxa	protein	261	24% helix, 23% strand	A0A0N7FW12
F	Putative metal-dependent isothiocyanate hydrolase saxa	protein	261	24% helix, 27% strand	A0A0N7FW12
H	Putative metal-dependent isothiocyanate hydrolase saxa	protein	256	23% helix, 24% strand	A0A0N7FW12

Ligands and binding sites

ZN · Zinc ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
FMT · Formic acid · additive · 4 copies · chains A, C, E, G

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	763	0.66	0.74	79	empty
2	562	0.66	0.76	42	empty
3	545	0.65	0.76	36	empty
4	524	0.64	0.76	36	empty
5	412	0.63	0.77	52	empty

Interfaces

16 interfaces between chains.

G–H · 999 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 894 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 880 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 877 Å² buried · 16 hydrogen bonds · protein-protein
F–G · 558 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6BRM · The crystal structure of isothiocyanate hydrolase from Delia radicum gut bacteria · the same entry in another collection · chain F against F, 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 A0A0N7FW12
Elsewhere: RCSB PDB 6BRM · PDBe 6BRM · UniProt A0A0N7FW12

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