Research workbench
An acetyl xylan esterase (EST2A) from the rumen bacterium butyrivibrio proteoclasticus.
Analyse An acetyl xylan esterase (EST2A) from the rumen bacterium butyrivibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DEV
- Type
- protein
- Length
- 2,980 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl-xylan esterase EST2A
- UniProt
- E0RVY7
- Ligands
- CL
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | Acetyl-xylan esterase EST2A | protein | 372 | 25% helix, 28% strand | E0RVY7 |
| D, F, G, H | Acetyl-xylan esterase EST2A | protein | 373 | 25% helix, 28% strand | E0RVY7 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
- ACY · Acetic acid · additive · 20 copies · chains A, H, B, C, D, E, F, G
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, D, E, G, H
- GOL · Glycerol · additive · 2 copies · chains C, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.75 | 0.78 | 152 | ACY |
| 2 | 655 | 0.73 | 0.80 | 102 | empty |
| 3 | 378 | 0.72 | 0.84 | 79 | empty |
| 4 | 814 | 0.72 | 0.78 | 83 | empty |
| 5 | 298 | 0.70 | 0.84 | 42 | empty |
Interfaces
12 interfaces between chains.
- A–F · 1299 Ų buried · 21 hydrogen bonds · protein-protein
- E–H · 1292 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1288 Ų buried · 22 hydrogen bonds · protein-protein
- C–G · 1288 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1162 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4DEV · An Acetyl Xylan Esterase (Est2A) from the Rumen Bacterium Butyrivibrio proteoclasticus. · 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 E0RVY7
- Elsewhere: RCSB PDB 4DEV · PDBe 4DEV · UniProt E0RVY7
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