MolNFT v1 · #77388 · protein
Protein crystal structure of xylanase A1 of paenibacillus sp. jdr-2
3RDK · Endo-1,4-beta-xylanase: “Protein crystal structure of xylanase A1 of paenibacillus sp. jdr-2”. X-ray diffraction, 5 ligands (GCV, XYP, XYS), 3 pockets (best druggability 0.78). MolNFT v1 #77388 on GenesisL1: 3D structure, binding…
- PDB
- 3RDK
- Type
- protein
- Length
- 667 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase
- EC
- 3.2.1.8
- UniProt
- C6CRV0
- Ligands
- GCV, XYP, XYS, MG, CL
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 333 | 46% helix, 20% strand | C6CRV0 |
| B | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 334 | 46% helix, 20% strand | C6CRV0 |
Ligands and binding sites
- GCV · 4-O-methyl-alpha-D-glucopyranuronic acid · ligand · 2 copies · chains B, A
- XYP · beta-D-xylopyranose · sugar · 4 copies · chains A, B
- XYS · alpha-D-xylopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 9 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 | 1127 | 0.78 | 0.80 | 95 | XYS, XYP, GOL, MG |
| 2 | 133 | 0.40 | 0.74 | 22 | empty |
| 3 | 53 | 0.25 | 0.72 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 660 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3RDK · Protein crystal structure of xylanase A1 of Paenibacillus sp. JDR-2 · the same entry in another collection · chain A against A, TM-score 1.00
- C6CRV0 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase a (C6CRV0) · a predicted model of the same protein · chain B 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 C6CRV0
- Elsewhere: RCSB PDB 3RDK · PDBe 3RDK · UniProt C6CRV0
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