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Crystal structure of PBGH5A, a glycoside hydrolase family 5 enzyme from prevotella bryantii B14, in complex with an inhibitory N- bromoacetylglycosylamine derivative of xxxg
Analyse Crystal structure of PBGH5A, a glycoside hydrolase family 5 enzyme from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D9P
- Type
- protein
- Length
- 694 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B-1,4-endoglucanase
- UniProt
- O06842
- Ligands
- NBG, BGC, XYS, CA
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | B-1,4-endoglucanase | protein | 347 | 44% helix, 13% strand | O06842 |
| B | B-1,4-endoglucanase | protein | 347 | 44% helix, 13% strand | O06842 |
Ligands and binding sites
- NBG · N-acetyl-beta-D-glucopyranosylamine · ligand · 4 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 12 copies · chains A, B
- XYS · alpha-D-xylopyranose · sugar · 12 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.59 | 0.76 | 52 | CA |
| 2 | 311 | 0.55 | 0.75 | 35 | NBG, XYS, BGC |
| 3 | 324 | 0.54 | 0.74 | 33 | NBG, BGC, XYS |
| 4 | 122 | 0.47 | 0.79 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 89 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5D9P · Crystal structure of PbGH5A, a glycoside hydrolase family 5 enzyme from Prevotella… · 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 O06842
- Elsewhere: RCSB PDB 5D9P · PDBe 5D9P · UniProt O06842
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