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The crystal structure of isothiocyanate hydrolase from delia radicum gut bacteria
Analyse The crystal structure of isothiocyanate hydrolase from delia radicum gut… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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.
| Volume (ų) | 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 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 894 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 880 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 877 Ų buried · 16 hydrogen bonds · protein-protein
- F–G · 558 Ų 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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