Research workbench
Crystal structure of the L-fucose isomerase soaked with MN2+ from raoultella sp.
Analyse Crystal structure of the L-fucose isomerase soaked with MN2+ from raoultella sp. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K1G
- Type
- protein
- Length
- 3,516 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-fucose isomerase
- EC
- 5.3.1.25
- UniProt
- A0A377T0E7
- Ligands
- MN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | L-fucose isomerase (EC 5.3.1.25) | protein | 586 | 40% helix, 20% strand | A0A377T0E7 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.86 | 0.87 | 130 | empty |
| 2 | 1034 | 0.85 | 0.86 | 88 | empty |
| 3 | 1189 | 0.85 | 0.86 | 116 | empty |
| 4 | 441 | 0.81 | 0.88 | 57 | empty |
| 5 | 193 | 0.81 | 0.95 | 41 | empty |
Interfaces
12 interfaces between chains.
- B–F · 2035 Ų buried · 28 hydrogen bonds · protein-protein
- B–E · 2032 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1997 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1994 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 1992 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6K1G · Crystal structure of the L-fucose isomerase soaked with Mn2+ from Raoultella sp. · 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 A0A377T0E7
- Elsewhere: RCSB PDB 6K1G · PDBe 6K1G · UniProt A0A377T0E7
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