MolNFT v1 · #24808 · protein
Crystal structure of xylanase from streptomyces olivaceoviridis E-86 complexed with 2(2)-alpha-L-arabinofuranosyl-xylobiose
1V6U · Endo-1,4-beta-D-xylanase: “Crystal structure of xylanase from streptomyces olivaceoviridis E-86 complexed with…”. X-ray diffraction, 3 ligands (XYP, AHR, XYS), 7 pockets (best druggability 0.65). MolNFT v1 #24808 on GenesisL1: 3D…
- PDB
- 1V6U
- Type
- protein
- Length
- 872 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-D-xylanase
- EC
- 3.2.1.8
- UniProt
- Q7SI98
- Ligands
- XYP, AHR, XYS
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endo-1,4-beta-D-xylanase (EC 3.2.1.8) | protein | 436 | 32% helix, 23% strand | Q7SI98 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 14 copies · chains A, B
- AHR · alpha-L-arabinofuranose · sugar · 2 copies · chains A, B
- XYS · alpha-D-xylopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.65 | 0.79 | 60 | empty |
| 2 | 524 | 0.64 | 0.76 | 65 | empty |
| 3 | 357 | 0.61 | 0.77 | 41 | empty |
| 4 | 74 | 0.37 | 0.77 | 18 | XYP |
| 5 | 64 | 0.30 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1035 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1V6U · Crystal Structure Of Xylanase From Streptomyces Olivaceoviridis E-86 Complexed With… · 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 1V6U · PDBe 1V6U · UniProt Q7SI98
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