Research workbench
Crystal structure of a loop truncation variant of thermotoga maritima acetyl esterase TM0077 (apo structure) at 2.75 ångström resolution
Analyse Crystal structure of a loop truncation variant of thermotoga maritima acetyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HFN
- Type
- protein
- Length
- 1,678 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
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 6 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cephalosporin-C deacetylase (EC 3.1.1.41, 3.1.1.72) | protein | 280 | 41% helix, 22% strand | Q9WXT2 |
| B | Cephalosporin-C deacetylase (EC 3.1.1.41, 3.1.1.72) | protein | 278 | 42% helix, 22% strand | Q9WXT2 |
| C | Cephalosporin-C deacetylase (EC 3.1.1.41, 3.1.1.72) | protein | 279 | 41% helix, 22% strand | Q9WXT2 |
| D | Cephalosporin-C deacetylase (EC 3.1.1.41, 3.1.1.72) | protein | 283 | 41% helix, 22% strand | Q9WXT2 |
| E | Cephalosporin-C deacetylase (EC 3.1.1.41, 3.1.1.72) | protein | 279 | 41% helix, 22% strand | Q9WXT2 |
| F | Cephalosporin-C deacetylase (EC 3.1.1.41, 3.1.1.72) | protein | 279 | 41% helix, 22% strand | Q9WXT2 |
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.66 | 0.76 | 52 | empty |
| 2 | 578 | 0.65 | 0.76 | 53 | empty |
| 3 | 561 | 0.64 | 0.76 | 53 | empty |
| 4 | 349 | 0.53 | 0.73 | 40 | empty |
| 5 | 66 | 0.49 | 0.85 | 16 | empty |
Interfaces
12 interfaces between chains.
- A–F · 986 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 981 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 974 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 582 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 481 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5HFN · Crystal structure of a loop truncation variant of Thermotoga maritima Acetyl Esterase… · 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 C 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 5HFN · PDBe 5HFN · UniProt Q9WXT2
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