Research workbench
Crystal structure of acetyl xylan esterase (TM0077) from thermotoga maritima at 2.12 a resolution (paraoxon inhibitor complex structure)
Analyse Crystal structure of acetyl xylan esterase (TM0077) from thermotoga maritima at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M83
- Type
- protein
- Length
- 1,948 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl xylan esterase
- UniProt
- Q9WXT2
- Ligands
- CA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F | Acetyl xylan esterase | protein | 325 | 35% helix, 19% strand | Q9WXT2 |
| D, E | Acetyl xylan esterase | protein | 324 | 35% helix, 19% strand | Q9WXT2 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, C, E, D, F
- ACT · Acetate ion · additive · 3 copies · chains A, C, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.78 | 0.80 | 68 | EDO |
| 2 | 1053 | 0.77 | 0.79 | 75 | EDO |
| 3 | 1182 | 0.76 | 0.78 | 65 | EDO |
| 4 | 384 | 0.63 | 0.78 | 43 | empty |
| 5 | 238 | 0.57 | 0.78 | 32 | empty |
Interfaces
12 interfaces between chains.
- B–D · 1117 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1110 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1107 Ų buried · 24 hydrogen bonds · protein-protein
- C–E · 1064 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 1055 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 3M83 · Crystal structure of Acetyl xylan esterase (TM0077) from THERMOTOGA MARITIMA at 2.12 A… · the same entry in another collection · chain E against E, TM-score 1.00
- Q9WXT2 · AlphaFold monomer V2.0 prediction for cephalosporin-C deacetylase (Q9WXT2) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q9WXT2
- Elsewhere: RCSB PDB 3M83 · PDBe 3M83 · UniProt Q9WXT2
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