MolNFT v1 · #116718 · protein
Crystal structure of the hexameric thioesterase Y2039 from yersinia pestis
5DM5 · Putative acyl-CoA thioester hydrolase: “Crystal structure of the hexameric thioesterase Y2039 from yersinia pestis”. X-ray diffraction, 9 pockets (best druggability 0.76). MolNFT v1 #116718 on GenesisL1: 3D structure, binding sites…
- PDB
- 5DM5
- Type
- protein
- Length
- 725 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative acyl-CoA thioester hydrolase
- EC
- 3.1.2.-
- UniProt
- Q7CIM6
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 18% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative acyl-CoA thioester hydrolase (EC 3.1.2.-) | protein | 117 | 20% helix, 44% strand | Q7CIM6 |
| B | Putative acyl-CoA thioester hydrolase (EC 3.1.2.-) | protein | 125 | 14% helix, 46% strand | Q7CIM6 |
| C | Putative acyl-CoA thioester hydrolase (EC 3.1.2.-) | protein | 121 | 19% helix, 48% strand | Q7CIM6 |
| D | Putative acyl-CoA thioester hydrolase (EC 3.1.2.-) | protein | 121 | 19% helix, 45% strand | Q7CIM6 |
| E | Putative acyl-CoA thioester hydrolase (EC 3.1.2.-) | protein | 119 | 19% helix, 48% strand | Q7CIM6 |
| F | Putative acyl-CoA thioester hydrolase (EC 3.1.2.-) | protein | 122 | 16% helix, 45% strand | Q7CIM6 |
Ligands and binding sites
- PGE · Triethylene glycol · additive · 3 copies · chains B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.76 | 0.86 | 45 | empty |
| 2 | 351 | 0.76 | 0.86 | 63 | empty |
| 3 | 224 | 0.74 | 0.88 | 36 | empty |
| 4 | 190 | 0.72 | 0.89 | 37 | empty |
| 5 | 258 | 0.72 | 0.86 | 39 | empty |
Interfaces
12 interfaces between chains.
- C–D · 918 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 868 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 864 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 725 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 697 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5DM5 · Crystal structure of the hexameric thioesterase y2039 from Yersinia pestis · 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 Q7CIM6
- Elsewhere: RCSB PDB 5DM5 · PDBe 5DM5 · UniProt Q7CIM6
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