MolNFT v1 · #141460 · protein
Structural of a novel B-glucosidase EMGH1 at 2.3 ångström from erythrobacter marinus
5Z87: “Structural of a novel B-glucosidase EMGH1 at 2.3 ångström from erythrobacter marinus”. X-ray diffraction, 2 ligands (BEN, MG), 11 pockets (best druggability 0.87). MolNFT v1 #141460 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5Z87
- Type
- protein
- Length
- 1,511 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EMGH1
- UniProt
- A0A0H0XV02
- Ligands
- BEN, MG
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | EMGH1 | protein | 756 | 33% helix, 19% strand | A0A0H0XV02 |
| B | EMGH1 | protein | 755 | 34% helix, 18% strand | A0A0H0XV02 |
Ligands and binding sites
- BEN · Benzamidine · ligand · chains B
- MG · Magnesium ion · metal · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.87 | 0.88 | 132 | MG, GOL, PEG |
| 2 | 706 | 0.73 | 0.79 | 76 | DTT |
| 3 | 643 | 0.73 | 0.80 | 72 | DTT |
| 4 | 154 | 0.48 | 0.77 | 30 | GOL |
| 5 | 160 | 0.47 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2942 Ų buried · 70 hydrogen bonds · protein-protein
Compared structures
- 5Z87 · Structural of a novel b-glucosidase EmGH1 at 2.3 angstrom from Erythrobacter marinus · 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 A0A0H0XV02
- Elsewhere: RCSB PDB 5Z87 · PDBe 5Z87 · UniProt A0A0H0XV02
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