MolNFT v1 · #25685 · protein
The 3-dimensional structure of a xylanase (XYN10A) from cellvibrio japonicus
1W2P · Endo-1,4-beta-xylanase a precursor: “The 3-dimensional structure of a xylanase (XYN10A) from cellvibrio japonicus”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.65). MolNFT v1 #25685 on GenesisL1: 3D structure…
- PDB
- 1W2P
- Type
- protein
- Length
- 692 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase a precursor
- EC
- 3.2.1.8
- UniProt
- P14768
- Ligands
- CA
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endo-1,4-beta-xylanase a precursor (EC 3.2.1.8) | protein | 346 | 39% helix, 20% strand | P14768 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.65 | 0.78 | 52 | empty |
| 2 | 280 | 0.60 | 0.79 | 35 | EDO |
| 3 | 219 | 0.52 | 0.76 | 31 | empty |
| 4 | 225 | 0.51 | 0.76 | 32 | empty |
| 5 | 86 | 0.43 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 432 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1W2P · The 3-dimensional structure of a xylanase (Xyn10A) from Cellvibrio japonicus · the same entry in another collection · chain A against A, TM-score 1.00
- P14768 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase a (P14768) · 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 P14768
- Elsewhere: RCSB PDB 1W2P · PDBe 1W2P · UniProt P14768
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