MolNFT v1 · #71115 · protein
Structural insights into the acidophilic pH adaptation of a novel endo-1,4-beta-xylanase from scytalidium acidophilum
3M4F: “Structural insights into the acidophilic pH adaptation of a novel endo-1,4-beta-xylanase from scytalidium…”. X-ray diffraction, 5 pockets (best druggability 0.73). MolNFT v1 #71115 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3M4F
- Type
- protein
- Length
- 724 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase
- EC
- 3.2.1.8
- UniProt
- Q6VAY1
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Endo-1,4-beta-xylanase (EC 3.2.1.8) | protein | 181 | 9% helix, 61% strand | Q6VAY1 |
Ligands and binding sites
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 696 | 0.73 | 0.80 | 85 | empty |
| 2 | 154 | 0.43 | 0.75 | 24 | CXS |
| 3 | 160 | 0.43 | 0.74 | 24 | CXS |
| 4 | 155 | 0.42 | 0.74 | 24 | CXS |
| 5 | 139 | 0.39 | 0.73 | 24 | CXS |
Interfaces
4 interfaces between chains.
- A–D · 355 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 355 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 350 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 330 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3M4F · Structural insights into the acidophilic pH adaptation of a novel endo-1,4-beta-xylanase… · 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 Q6VAY1
- Elsewhere: RCSB PDB 3M4F · PDBe 3M4F · UniProt Q6VAY1
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