Research workbench
Crystal structure of the thermotoga maritima acetyl esterase (TM0077) complex with a substrate analog
Analyse Crystal structure of the thermotoga maritima acetyl esterase (TM0077) complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JIB
- Type
- protein
- Length
- 1,916 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
- OIA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Cephalosporin-C deacetylase (EC 3.1.1.41, 3.1.1.72) | protein | 319 | 37% helix, 20% strand | Q9WXT2 |
| C, F | Cephalosporin-C deacetylase (EC 3.1.1.41, 3.1.1.72) | protein | 320 | 37% helix, 20% strand | Q9WXT2 |
| E | Cephalosporin-C deacetylase (EC 3.1.1.41, 3.1.1.72) | protein | 319 | 35% helix, 20% strand | Q9WXT2 |
Ligands and binding sites
- OIA · [(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]acetic acid · ligand · 6 copies · chains A, B, C, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 924 | 0.76 | 0.79 | 64 | empty |
| 2 | 940 | 0.75 | 0.78 | 66 | empty |
| 3 | 826 | 0.74 | 0.78 | 62 | empty |
| 4 | 62 | 0.64 | 0.93 | 23 | empty |
| 5 | 165 | 0.49 | 0.77 | 25 | empty |
Interfaces
12 interfaces between chains.
- C–F · 1120 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1113 Ų buried · 24 hydrogen bonds · protein-protein
- B–E · 1110 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1067 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 1066 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5JIB · Crystal structure of the Thermotoga maritima acetyl esterase (TM0077) complex with a… · 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 5JIB · PDBe 5JIB · UniProt Q9WXT2
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