MolNFT v1 · #189358 · protein
The structure of beta-xylosidase from phanerochaete CHRYSOSPORIUM(PCBXL3)
7VC7 · Xylan 1,4-beta-xylosidase: “The structure of beta-xylosidase from phanerochaete CHRYSOSPORIUM(PCBXL3)”. X-ray diffraction, 2 ligands (NAG, XYP), 4 pockets (best druggability 0.72). MolNFT v1 #189358 on GenesisL1: 3D structure…
- PDB
- 7VC7
- Type
- protein
- Length
- 743 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylan 1,4-beta-xylosidase
- EC
- 3.2.1.37
- Ligands
- NAG, XYP
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylan 1,4-beta-xylosidase (EC 3.2.1.37) | protein | 743 | 31% helix, 19% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- XYP · beta-D-xylopyranose · sugar · chains A
- 1PE · Pentaethylene glycol · additive · 12 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.72 | 0.85 | 45 | 1PE |
| 2 | 57 | 0.34 | 0.78 | 15 | empty |
| 3 | 61 | 0.33 | 0.77 | 20 | empty |
| 4 | 52 | 0.28 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 7 glycan, 4 disulfide, 2 covalent (N-glycosylation, disulfide, additive adduct).
Compared structures
- 7VC7 · The structure of beta-xylosidase from Phanerochaete chrysosporium(PcBxl3) · 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
- Elsewhere: RCSB PDB 7VC7 · PDBe 7VC7
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