MolNFT v1 · #116960 · protein
Crystal structure of M. tuberculosis ECHA6 bound to C20-CoA
5DTW · Enoyl-CoA hydratase ECHA6: “Crystal structure of M. tuberculosis ECHA6 bound to C20-CoA”. X-ray diffraction, 1 ligand (5F9), 10 pockets (best druggability 0.81). MolNFT v1 #116960 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5DTW
- Type
- protein
- Length
- 1,457 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enoyl-CoA hydratase ECHA6
- EC
- 4.2.1.17
- UniProt
- P9WNP1
- Ligands
- 5F9
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F | Enoyl-CoA hydratase ECHA6 (EC 4.2.1.17) | protein | 244 | 47% helix, 16% strand | P9WNP1 |
| B | Enoyl-CoA hydratase ECHA6 (EC 4.2.1.17) | protein | 240 | 48% helix, 16% strand | P9WNP1 |
| C | Enoyl-CoA hydratase ECHA6 (EC 4.2.1.17) | protein | 246 | 46% helix, 16% strand | P9WNP1 |
| E | Enoyl-CoA hydratase ECHA6 (EC 4.2.1.17) | protein | 239 | 48% helix, 16% strand | P9WNP1 |
Ligands and binding sites
- 5F9 · Arachinoyl-CoA · ligand · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.81 | 0.85 | 53 | empty |
| 2 | 670 | 0.81 | 0.86 | 48 | empty |
| 3 | 1117 | 0.80 | 0.81 | 116 | 5F9 |
| 4 | 463 | 0.63 | 0.76 | 46 | empty |
| 5 | 462 | 0.62 | 0.75 | 42 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1431 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1410 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1405 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1399 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 1398 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5DTW · Crystal structure of M. tuberculosis EchA6 bound to C20-CoA · the same entry in another collection · chain F against F, TM-score 1.00
- P9WNP1 · AlphaFold monomer V2.0 prediction for probable enoyl-CoA hydratase ECHA6 (P9WNP1) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P9WNP1
- Elsewhere: RCSB PDB 5DTW · PDBe 5DTW · UniProt P9WNP1
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