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The carbohydrate binding module family 48 (CBM48) and carboxy-terminal carbohydrate esterase family 1 (CE1) domains of the multidomain esterase DMCE1B from dysgonomonas mossii
Analyse The carbohydrate binding module family 48 (CBM48) and carboxy-terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B5V
- Type
- protein
- Length
- 698 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbohydrate esterase family 1 protein with an N-terminal carbohydrate binding module…
- UniProt
- F8X1N1
- Ligands
- CL
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbohydrate esterase family 1 protein with an N-terminal carbohydrate binding module family 48 | protein | 350 | 27% helix, 29% strand | F8X1N1 |
| B | Carbohydrate esterase family 1 protein with an N-terminal carbohydrate binding module family 48 | protein | 348 | 26% helix, 30% strand | F8X1N1 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.80 | 0.82 | 82 | empty |
| 2 | 178 | 0.51 | 0.78 | 34 | empty |
| 3 | 110 | 0.46 | 0.79 | 25 | empty |
| 4 | 138 | 0.43 | 0.75 | 32 | empty |
| 5 | 154 | 0.42 | 0.74 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1724 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7B5V · The carbohydrate binding module family 48 (CBM48) and carboxy-terminal carbohydrate… · 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 F8X1N1
- Elsewhere: RCSB PDB 7B5V · PDBe 7B5V · UniProt F8X1N1
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