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Crystal structure of MSMEG_1712 from mycobacterium smegmatis in complex with beta-D-fucofuranose
Analyse Crystal structure of MSMEG_1712 from mycobacterium smegmatis in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HYH
- Type
- protein
- Length
- 608 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic binding PROTEIN/LACI transcriptional regulator
- UniProt
- I7G686
- Ligands
- GYE, ZN
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Periplasmic binding PROTEIN/LACI transcriptional regulator | protein | 304 | 45% helix, 21% strand | I7G686 |
Ligands and binding sites
- GYE · beta-D-fucofuranose · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 695 | 0.73 | 0.79 | 73 | ZN |
| 2 | 154 | 0.67 | 0.87 | 31 | ZN |
| 3 | 391 | 0.61 | 0.77 | 46 | empty |
| 4 | 58 | 0.37 | 0.80 | 22 | empty |
| 5 | 54 | 0.34 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 911 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6HYH · Crystal structure of MSMEG_1712 from Mycobacterium smegmatis in complex with… · 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 I7G686
- Elsewhere: RCSB PDB 6HYH · PDBe 6HYH · UniProt I7G686
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