MolNFT v1 · #7900 · protein
S954A mutant of the feruloyl esterase module from clostridium thermocellum complexed with ferulic acid
1GKL · Endo-1,4-beta-xylanase Y: “S954A mutant of the feruloyl esterase module from clostridium thermocellum complexed with ferulic acid”. X-ray diffraction, 2 ligands (FER, CD), 6 pockets (best druggability 0.45). MolNFT v1 #7900 on…
- PDB
- 1GKL
- Type
- protein
- Length
- 566 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase Y
- EC
- 3.2.1.8
- UniProt
- P51584
- Ligands
- FER, CD
- Pockets
- 6 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endo-1,4-beta-xylanase Y (EC 3.2.1.8) | protein | 283 | 33% helix, 20% strand | P51584 |
Ligands and binding sites
- FER · 3-(4-hydroxy-3-methoxyphenyl)-2-propenoic acid · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 12 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.45 | 0.81 | 22 | empty |
| 2 | 92 | 0.40 | 0.77 | 17 | empty |
| 3 | 68 | 0.38 | 0.78 | 14 | empty |
| 4 | 88 | 0.37 | 0.76 | 12 | empty |
| 5 | 91 | 0.37 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1030 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 1GKL · S954A mutant of the feruloyl esterase module from clostridium thermocellum complexed with… · the same entry in another collection · chain B against B, TM-score 1.00
- P51584 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase Y (P51584) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P51584
- Elsewhere: RCSB PDB 1GKL · PDBe 1GKL · UniProt P51584
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