Research workbench
Structural characterisation of mutant ASP39ALA of thioesterase (nmach) from neisseria meningitidis
Analyse Structural characterisation of mutant ASP39ALA of thioesterase (nmach) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T02
- Type
- protein
- Length
- 883 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA hydrolase
- EC
- 3.1.2.-
- UniProt
- A0A0Y5D4F5
- Ligands
- GDP, COA, CL
- Pockets
- 18 · best druggability 0.65
Structure
x-ray diffraction · 6 distinct chains · 28% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA hydrolase (EC 3.1.2.-) | protein | 146 | 27% helix, 39% strand | A0A0Y5D4F5 |
| B | Acyl-CoA hydrolase (EC 3.1.2.-) | protein | 147 | 29% helix, 40% strand | A0A0Y5D4F5 |
| C | Acyl-CoA hydrolase (EC 3.1.2.-) | protein | 150 | 28% helix, 39% strand | A0A0Y5D4F5 |
| D | Acyl-CoA hydrolase (EC 3.1.2.-) | protein | 148 | 27% helix, 39% strand | A0A0Y5D4F5 |
| E | Acyl-CoA hydrolase (EC 3.1.2.-) | protein | 147 | 27% helix, 39% strand | A0A0Y5D4F5 |
| F | Acyl-CoA hydrolase (EC 3.1.2.-) | protein | 145 | 28% helix, 39% strand | A0A0Y5D4F5 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- COA · Coenzyme A · ligand · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 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
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.65 | 0.78 | 59 | GDP |
| 2 | 202 | 0.61 | 0.82 | 26 | CL, COA |
| 3 | 139 | 0.61 | 0.85 | 26 | COA, CL |
| 4 | 228 | 0.56 | 0.79 | 30 | GDP |
| 5 | 105 | 0.56 | 0.84 | 19 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1377 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1109 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 985 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 575 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 185 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5T02 · Structural characterisation of mutant Asp39Ala of thioesterase (NmACH) from Neisseria… · the same entry in another collection · chain A 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 A0A0Y5D4F5
- Elsewhere: RCSB PDB 5T02 · PDBe 5T02 · UniProt A0A0Y5D4F5
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