MolNFT v1 · #21309 · protein
Crystal structure of hypothetical protein EC709 from escherichia COLI
1S5U · Protein ybgc: “Crystal structure of hypothetical protein EC709 from escherichia COLI”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.87). MolNFT v1 #21309 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1S5U
- Type
- protein
- Length
- 1,042 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein ybgc
- UniProt
- P0A8Z3
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Protein ybgc | protein | 129 | 26% helix, 42% strand | P0A8Z3 |
| B | Protein ybgc | protein | 128 | 24% helix, 41% strand | P0A8Z3 |
| C, F | Protein ybgc | protein | 130 | 26% helix, 41% strand | P0A8Z3 |
| E | Protein ybgc | protein | 136 | 24% helix, 40% strand | P0A8Z3 |
| G, H | Protein ybgc | protein | 130 | 25% helix, 40% strand | P0A8Z3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, C, E, H, F, G, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.87 | 0.96 | 37 | empty |
| 2 | 406 | 0.87 | 0.96 | 36 | empty |
| 3 | 886 | 0.81 | 0.83 | 104 | EDO |
| 4 | 238 | 0.77 | 0.90 | 36 | empty |
| 5 | 352 | 0.77 | 0.87 | 45 | empty |
Interfaces
15 interfaces between chains.
- A–B · 954 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 878 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 858 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 855 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 806 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1S5U · Crystal Structure of Hypothetical Protein EC709 from Escherichia coli · the same entry in another collection · chain H against H, TM-score 1.00
- P0A8Z3 · AlphaFold monomer V2.0 prediction for acyl-CoA thioester hydrolase ybgc (P0A8Z3) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P0A8Z3
- Elsewhere: RCSB PDB 1S5U · PDBe 1S5U · UniProt P0A8Z3
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