MolNFT v1 · #120122 · protein
Crystal structure of covalent glycosyl-enzyme intermediate of xylanase mutant (T82A, N127S, and E128H) from streptomyces olivaceoviridis E- 86
5GQD · Beta-xylanase: “Crystal structure of covalent glycosyl-enzyme intermediate of xylanase mutant (T82A, N127S, and E128H) from…”. X-ray diffraction, 2 ligands (XYS, XYP), 6 pockets (best druggability 0.66). MolNFT v1 #120122 on…
- PDB
- 5GQD
- Type
- protein
- Length
- 854 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylanase
- EC
- 3.2.1.8
- UniProt
- Q7SI98
- Ligands
- XYS, XYP
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-xylanase (EC 3.2.1.8) | protein | 427 | 34% helix, 24% strand | Q7SI98 |
Ligands and binding sites
- XYS · alpha-D-xylopyranose · sugar · 2 copies · chains A, B
- XYP · beta-D-xylopyranose · sugar · 2 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.66 | 0.80 | 44 | GOL |
| 2 | 115 | 0.36 | 0.73 | 24 | empty |
| 3 | 81 | 0.34 | 0.75 | 20 | XYS, XYP, GOL |
| 4 | 61 | 0.31 | 0.75 | 19 | XYS, XYP |
| 5 | 68 | 0.28 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1030 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, glycosylation).
Compared structures
- 5GQD · Crystal structure of covalent glycosyl-enzyme intermediate of xylanase mutant (T82A… · 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 Q7SI98
- Elsewhere: RCSB PDB 5GQD · PDBe 5GQD · UniProt Q7SI98
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