MolNFT v1 · #120006 · protein
Crystal structure of the P228A variant of thermotoga maritima acetyl esterase
5GMA · Cephalosporin-C deacetylase: “Crystal structure of the P228A variant of thermotoga maritima acetyl esterase”. X-ray diffraction, 20 pockets (best druggability 0.75). MolNFT v1 #120006 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5GMA
- Type
- protein
- Length
- 1,942 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 0.75
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 | 323 | 35% helix, 20% strand | Q9WXT2 |
| B, C, E, F | Cephalosporin-C deacetylase (EC 3.1.1.41, 3.1.1.72) | protein | 324 | 36% helix, 19% strand | Q9WXT2 |
Ligands and binding sites
- ACT · Acetate ion · additive · 3 copies · chains C, F, A, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.75 | 0.78 | 60 | empty |
| 2 | 853 | 0.75 | 0.79 | 62 | empty |
| 3 | 919 | 0.75 | 0.78 | 63 | empty |
| 4 | 251 | 0.53 | 0.76 | 26 | empty |
| 5 | 216 | 0.52 | 0.76 | 22 | empty |
Interfaces
12 interfaces between chains.
- A–D · 1126 Ų buried · 23 hydrogen bonds · protein-protein
- C–F · 1125 Ų buried · 22 hydrogen bonds · protein-protein
- B–E · 1117 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1069 Ų buried · 9 hydrogen bonds · protein-protein
- C–E · 1060 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5GMA · Crystal structure of the P228A 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 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 5GMA · PDBe 5GMA · UniProt Q9WXT2
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