Research workbench
Xylanase XYN10A from streptomyces lividans in complex with xylobio- isofagomine at pH 7.5
Analyse Xylanase XYN10A from streptomyces lividans in complex with xylobio- isofagomine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V0N
- Type
- protein
- Length
- 302 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase a
- EC
- 3.2.1.8
- UniProt
- P26514
- Ligands
- XIF, XYP
- Pockets
- 1 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-1,4-beta-xylanase a (EC 3.2.1.8) | protein | 302 | 42% helix, 20% strand | P26514 |
Ligands and binding sites
- XIF · Piperidine-3,4-diol · ligand · chains A
- XYP · beta-D-xylopyranose · sugar · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.35 | 0.76 | 19 | XIF, XYP, IMD |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1V0N · Xylanase Xyn10a from Streptomyces lividans in complex with xylobio-isofagomine at pH 7.5 · the same entry in another collection · chain A against A, TM-score 1.00
- P26514 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase a (P26514) · a predicted model of the same protein · 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 P26514
- Elsewhere: RCSB PDB 1V0N · PDBe 1V0N · UniProt P26514
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