Research workbench
Crystal structure of the monoclinic form of thermotoga maritima acetyl esterase TM0077 (apo structure) at 1.76 ångström resolution
Analyse Crystal structure of the monoclinic form of thermotoga maritima acetyl esterase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FDF
- Type
- protein
- Length
- 1,918 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cephalosporin-C deacetylase
- EC
- 3.1.1.41, 3.1.1.72
- UniProt
- Q9WXT2
- Ligands
- CL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Cephalosporin-C deacetylase (EC 3.1.1.41, 3.1.1.72) | protein | 319 | 36% helix, 20% strand | Q9WXT2 |
| B, C, E, F | Cephalosporin-C deacetylase (EC 3.1.1.41, 3.1.1.72) | protein | 320 | 37% helix, 20% strand | Q9WXT2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.76 | 0.78 | 64 | empty |
| 2 | 913 | 0.75 | 0.78 | 65 | empty |
| 3 | 814 | 0.74 | 0.78 | 65 | empty |
| 4 | 69 | 0.62 | 0.91 | 25 | empty |
| 5 | 71 | 0.51 | 0.85 | 15 | empty |
Interfaces
12 interfaces between chains.
- C–F · 1138 Ų buried · 25 hydrogen bonds · protein-protein
- B–E · 1122 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1113 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 1056 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 1053 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5FDF · Crystal structure of the monoclinic form of Thermotoga maritima Acetyl Esterase TM0077… · the same entry in another collection · chain F against F, 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 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 Q9WXT2
- Elsewhere: RCSB PDB 5FDF · PDBe 5FDF · UniProt Q9WXT2
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