MolNFT v1 · #176231 · protein
Crystal structure of glycoside hydrolase family 11 beta-xylanase from streptomyces olivaceoviridis E-86 in complex with 4-O-methyl-alpha-D- glucuronopyranosyl xylotetraose
7DFO · Endo-1,4-beta-xylanase: “Crystal structure of glycoside hydrolase family 11 beta-xylanase from streptomyces olivaceoviridis E-86 in…”. X-ray diffraction, 4 ligands (GCV, XYP, NA), 17 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 7DFO
- Type
- protein
- Length
- 1,745 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase
- EC
- 3.2.1.8
- Ligands
- GCV, XYP, NA, CL
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, G, H, I | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 194 | 5% helix, 65% strand | — |
| C | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 193 | 5% helix, 65% strand | — |
Ligands and binding sites
- GCV · 4-O-methyl-alpha-D-glucopyranuronic acid · ligand · 3 copies · chains B, C, F
- XYP · beta-D-xylopyranose · sugar · 25 copies · chains A, B, C, E, F, G, I
- NA · Sodium ion · metal · 13 copies · chains A, B, C, D, E, F, I
- CL · Chloride ion · ion · 43 copies · chains A, D, B, C, I, G, H, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.77 | 0.80 | 106 | CL |
| 2 | 364 | 0.76 | 0.86 | 45 | XYP |
| 3 | 347 | 0.75 | 0.86 | 47 | XYP |
| 4 | 341 | 0.73 | 0.85 | 47 | empty |
| 5 | 267 | 0.70 | 0.85 | 52 | CL |
Interfaces
13 interfaces between chains.
- C–D · 710 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 707 Ų buried · 7 hydrogen bonds · protein-protein
- C–I · 692 Ų buried · 14 hydrogen bonds · protein-protein
- E–H · 643 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 574 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7DFO · Crystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces… · 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 7DFO · PDBe 7DFO
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