Research workbench
Structure of a fucose lectin from kordia zhangzhouensis in complex with methyl-fucoside
Analyse Structure of a fucose lectin from kordia zhangzhouensis 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
- 6HTN
- Type
- protein
- Length
- 858 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucose-binding lectin
- UniProt
- A0A2T6C3M6
- Ligands
- MFU
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Fucose-binding lectin | protein | 143 | 0% helix, 50% strand | A0A2T6C3M6 |
Ligands and binding sites
- MFU · methyl alpha-L-fucopyranoside · ligand · 18 copies · chains A, B, C, D, E, F
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, E
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.78 | 0.88 | 71 | MRD |
| 2 | 615 | 0.72 | 0.80 | 58 | MFU |
| 3 | 227 | 0.72 | 0.88 | 36 | empty |
| 4 | 102 | 0.60 | 0.87 | 24 | empty |
| 5 | 112 | 0.58 | 0.85 | 30 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1337 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1301 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 375 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 355 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 349 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6HTN · Structure of a fucose lectin from Kordia zhangzhouensis in complex with methyl-fucoside · 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 A0A2T6C3M6
- Elsewhere: RCSB PDB 6HTN · PDBe 6HTN · UniProt A0A2T6C3M6
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