MolNFT v1 · #16924 · protein
Xylanase XYN10A from streptomyces lividans in complex with xylobio- isofagomine lactam
1OD8 · Endo-1,4-beta-xylanase a: “Xylanase XYN10A from streptomyces lividans in complex with xylobio- isofagomine lactam”. X-ray diffraction, 3 ligands (XDL, XYP, NA), 1 pocket (best druggability 0.33). MolNFT v1 #16924 on GenesisL1: 3D…
- PDB
- 1OD8
- Type
- protein
- Length
- 301 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
- XDL, XYP, NA
- Pockets
- 1 · best druggability 0.33
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-1,4-beta-xylanase a (EC 3.2.1.8) | protein | 301 | 42% helix, 19% strand | P26514 |
Ligands and binding sites
- XDL · Xylose-derived isofagomine lactam · ligand · 2 copies · chains A
- XYP · beta-D-xylopyranose · sugar · 2 copies · chains A
- NA · Sodium ion · metal · 4 copies · chains A
- IMD · Imidazole · additive · 2 copies · 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 | 67 | 0.33 | 0.76 | 19 | XYP, IMD, XDL |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1OD8 · Xylanase Xyn10A from Streptomyces lividans in complex with xylobio-isofagomine lactam · 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 1OD8 · PDBe 1OD8 · UniProt P26514
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