Research workbench
Crystal structure of TT0143 from thermus thermophilus HB8
Analyse Crystal structure of TT0143 from thermus thermophilus HB8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YW9
- Type
- protein
- Length
- 1,978 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enoyl-[acyl carrier protein] reductase
- EC
- 1.3.1.10
- UniProt
- Q5SLI9
- Ligands
- NAP
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 7 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enoyl-[acyl carrier protein] reductase (EC 1.3.1.10) | protein | 242 | 48% helix, 21% strand | Q5SLI9 |
| B, G | Enoyl-[acyl carrier protein] reductase (EC 1.3.1.10) | protein | 255 | 49% helix, 19% strand | Q5SLI9 |
| C | Enoyl-[acyl carrier protein] reductase (EC 1.3.1.10) | protein | 245 | 48% helix, 20% strand | Q5SLI9 |
| D | Enoyl-[acyl carrier protein] reductase (EC 1.3.1.10) | protein | 247 | 49% helix, 19% strand | Q5SLI9 |
| E | Enoyl-[acyl carrier protein] reductase (EC 1.3.1.10) | protein | 246 | 49% helix, 20% strand | Q5SLI9 |
| F | Enoyl-[acyl carrier protein] reductase (EC 1.3.1.10) | protein | 242 | 49% helix, 20% strand | Q5SLI9 |
| H | Enoyl-[acyl carrier protein] reductase (EC 1.3.1.10) | protein | 246 | 50% helix, 20% strand | Q5SLI9 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1107 | 0.84 | 0.85 | 56 | empty |
| 2 | 1151 | 0.84 | 0.85 | 61 | empty |
| 3 | 415 | 0.79 | 0.87 | 57 | empty |
| 4 | 386 | 0.78 | 0.87 | 55 | empty |
| 5 | 473 | 0.66 | 0.78 | 43 | NAP |
Interfaces
15 interfaces between chains.
- E–F · 1875 Ų buried · 44 hydrogen bonds · protein-protein
- G–H · 1874 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 1873 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 1851 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 1744 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 2YW9 · Crystal structure of TT0143 from Thermus thermophilus HB8 · 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 Q5SLI9
- Elsewhere: RCSB PDB 2YW9 · PDBe 2YW9 · UniProt Q5SLI9
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