MolNFT v1 · #134775 · protein
Crystal structure of glycosil hydrolase family 3 N-terminal domain protein from bacteroides intestinalis
5TF0 · Glycosyl hydrolase family 3 N-terminal domain protein: “Crystal structure of glycosil hydrolase family 3 N-terminal domain protein from bacteroides intestinalis”. X-ray diffraction, 1 ligand (MG), 14 pockets (best druggability…
- PDB
- 5TF0
- Type
- protein
- Length
- 1,466 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase family 3 N-terminal domain protein
- UniProt
- B3C777
- Ligands
- MG
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl hydrolase family 3 N-terminal domain protein | protein | 733 | 34% helix, 20% strand | B3C777 |
| B | Glycosyl hydrolase family 3 N-terminal domain protein | protein | 733 | 32% helix, 20% strand | B3C777 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.85 | 0.97 | 36 | empty |
| 2 | 466 | 0.74 | 0.83 | 75 | empty |
| 3 | 296 | 0.65 | 0.81 | 39 | EDO |
| 4 | 149 | 0.58 | 0.82 | 27 | empty |
| 5 | 221 | 0.57 | 0.79 | 29 | EDO |
Interfaces
1 interface between chains.
- A–B · 3483 Ų buried · 87 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 modified (engineered).
Compared structures
- 5TF0 · Crystal Structure of Glycosil Hydrolase Family 3 N-Terminal Domain Protein from… · 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 B3C777
- Elsewhere: RCSB PDB 5TF0 · PDBe 5TF0 · UniProt B3C777
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