Research workbench
Crystal structure of putative glucoamylase (YP_210071.1) from bacteroides fragilis nctc 9343 at 2.12 a resolution
Analyse Crystal structure of putative glucoamylase (YP_210071.1) from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EU8
- Type
- protein
- Length
- 1,688 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative glucoamylase
- UniProt
- Q5LIB7
- Ligands
- K, CL
- Pockets
- 13 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative glucoamylase | protein | 422 | 45% helix, 15% strand | Q5LIB7 |
Ligands and binding sites
- K · Potassium ion · metal · 5 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 84 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.69 | 0.79 | 63 | EDO |
| 2 | 392 | 0.62 | 0.77 | 59 | empty |
| 3 | 388 | 0.60 | 0.76 | 53 | EDO |
| 4 | 357 | 0.59 | 0.76 | 41 | EDO |
| 5 | 276 | 0.55 | 0.76 | 37 | EDO |
Interfaces
4 interfaces between chains.
- A–B · 970 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 352 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 303 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 60 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 3EU8 · Crystal structure of putative glucoamylase (YP_210071.1) from Bacteroides fragilis NCTC… · 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 Q5LIB7
- Elsewhere: RCSB PDB 3EU8 · PDBe 3EU8 · UniProt Q5LIB7
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