MolNFT v1 · #104592 · protein
Crystal structure of an enoyl-CoA hydratase from mycobacterium smegmatis
4QFE: “Crystal structure of an enoyl-CoA hydratase from mycobacterium smegmatis”. X-ray diffraction, 2 ligands (NA, PO4), 20 pockets (best druggability 0.79). MolNFT v1 #104592 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4QFE
- Type
- protein
- Length
- 2,731 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enoyl-CoA hydratase
- EC
- 4.2.1.17
- UniProt
- A0QS88
- Ligands
- NA, PO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 10 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enoyl-CoA hydratase (EC 4.2.1.17) | protein | 225 | 39% helix, 20% strand | A0QS88 |
| B, I | Enoyl-CoA hydratase (EC 4.2.1.17) | protein | 228 | 41% helix, 20% strand | A0QS88 |
| C | Enoyl-CoA hydratase (EC 4.2.1.17) | protein | 229 | 41% helix, 19% strand | A0QS88 |
| D | Enoyl-CoA hydratase (EC 4.2.1.17) | protein | 230 | 42% helix, 20% strand | A0QS88 |
| E | Enoyl-CoA hydratase (EC 4.2.1.17) | protein | 225 | 40% helix, 20% strand | A0QS88 |
| F | Enoyl-CoA hydratase (EC 4.2.1.17) | protein | 226 | 41% helix, 19% strand | A0QS88 |
| G, H | Enoyl-CoA hydratase (EC 4.2.1.17) | protein | 227 | 41% helix, 19% strand | A0QS88 |
| J | Enoyl-CoA hydratase (EC 4.2.1.17) | protein | 228 | 42% helix, 19% strand | A0QS88 |
| K | Enoyl-CoA hydratase (EC 4.2.1.17) | protein | 229 | 42% helix, 19% strand | A0QS88 |
| L | Enoyl-CoA hydratase (EC 4.2.1.17) | protein | 229 | 41% helix, 19% strand | A0QS88 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, D, F, B, E, H, G, I, L, C, J, K
- PO4 · Phosphate ion · ion · 4 copies · chains B, E, H, G, I, L, A, D, F
- EDO · 1,2-ethanediol · additive · 32 copies · chains A, B, H, D, E, F, G, I, L, J, K, C
- EOH · Ethanol · additive · 2 copies · chains B, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.79 | 0.82 | 99 | EDO |
| 2 | 807 | 0.75 | 0.79 | 117 | EDO |
| 3 | 504 | 0.71 | 0.81 | 62 | EDO |
| 4 | 147 | 0.70 | 0.90 | 25 | empty |
| 5 | 74 | 0.70 | 0.96 | 34 | PO4 |
Interfaces
20 interfaces between chains.
- J–K · 1586 Ų buried · 32 hydrogen bonds · protein-protein
- G–I · 1556 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 1534 Ų buried · 32 hydrogen bonds · protein-protein
- C–K · 1532 Ų buried · 33 hydrogen bonds · protein-protein
- C–J · 1516 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 4QFE · Crystal Structure of an Enoyl-CoA hydratase from Mycobacterium smegmatis · 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 A0QS88
- Elsewhere: RCSB PDB 4QFE · PDBe 4QFE · UniProt A0QS88
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