MolNFT v1 · #116972 · protein
Crystal structure of M. tuberculosis ECHA6 bound to GSK572A
5DU8 · Probable enoyl-CoA hydratase ECHA6: “Crystal structure of M. tuberculosis ECHA6 bound to GSK572A”. X-ray diffraction, 1 ligand (5FK), 8 pockets (best druggability 0.81). MolNFT v1 #116972 on GenesisL1: 3D structure, binding sites…
- PDB
- 5DU8
- Type
- protein
- Length
- 719 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable enoyl-CoA hydratase ECHA6
- EC
- 4.2.1.17
- UniProt
- P9WNP1
- Ligands
- 5FK
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable enoyl-CoA hydratase ECHA6 (EC 4.2.1.17) | protein | 234 | 48% helix, 17% strand | P9WNP1 |
| B | Probable enoyl-CoA hydratase ECHA6 (EC 4.2.1.17) | protein | 241 | 47% helix, 16% strand | P9WNP1 |
| C | Probable enoyl-CoA hydratase ECHA6 (EC 4.2.1.17) | protein | 244 | 49% helix, 16% strand | P9WNP1 |
Ligands and binding sites
- 5FK · (5R,7S)-5-(4-ethylphenyl)-N-[(5-fluoropyridin-2-yl)methyl]-7-(trifluoromethyl)-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidine-3-carboxamide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.81 | 0.86 | 48 | empty |
| 2 | 501 | 0.66 | 0.77 | 48 | 5FK |
| 3 | 522 | 0.64 | 0.76 | 45 | 5FK |
| 4 | 375 | 0.58 | 0.75 | 42 | 5FK |
| 5 | 60 | 0.42 | 0.82 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1436 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1428 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1400 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5DU8 · Crystal structure of M. tuberculosis EchA6 bound to GSK572A · the same entry in another collection · chain A against A, 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 5DU8 · PDBe 5DU8 · UniProt P9WNP1
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