MolNFT v1 · #129909 · protein
GH5 endo-xyloglucanase from cellvibrio japonicus
5OYD · Cellulase, putative, CEL5D: “GH5 endo-xyloglucanase from cellvibrio japonicus”. X-ray diffraction, 5 ligands (NBG, BGC, XYS), 3 pockets (best druggability 0.71). MolNFT v1 #129909 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5OYD
- Type
- protein
- Length
- 741 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellulase, putative, CEL5D
- EC
- 3.2.1.151
- UniProt
- B3PD52
- Ligands
- NBG, BGC, XYS, CL, SO4
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellulase, putative, CEL5D (EC 3.2.1.151) | protein | 370 | 40% helix, 12% strand | B3PD52 |
| B | Cellulase, putative, CEL5D (EC 3.2.1.151) | protein | 371 | 40% helix, 13% strand | B3PD52 |
Ligands and binding sites
- NBG · N-acetyl-beta-D-glucopyranosylamine · ligand · 2 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 6 copies · chains A, B
- XYS · alpha-D-xylopyranose · sugar · 5 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.71 | 0.75 | 106 | NBG, BGC, XYS |
| 2 | 146 | 0.45 | 0.76 | 23 | empty |
| 3 | 70 | 0.33 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 711 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5OYD · GH5 endo-xyloglucanase from Cellvibrio japonicus · 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 B3PD52
- Elsewhere: RCSB PDB 5OYD · PDBe 5OYD · UniProt B3PD52
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