MolNFT v1 · #26448 · protein
Structure of escherichia COLI yfbu gene product
1WPB · Hypothetical protein yfbu: “Structure of escherichia COLI yfbu gene product”. X-ray diffraction, 1 ligand (CL), 17 pockets (best druggability 0.47). MolNFT v1 #26448 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1WPB
- Type
- protein
- Length
- 2,687 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein yfbu
- UniProt
- Q1R9C1
- Ligands
- CL
- Pockets
- 17 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, N, O, P | Hypothetical protein yfbu | protein | 168 | 61% helix, 1% strand | Q1R9C1 |
| M | Hypothetical protein yfbu | protein | 167 | 62% helix, 1% strand | Q1R9C1 |
Ligands and binding sites
- CL · Chloride ion · ion · 36 copies · chains A, B, C, G, D, H, E, F, I, M, J, N, K, O, L, P
- GOL · Glycerol · additive · 44 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.47 | 0.73 | 32 | empty |
| 2 | 214 | 0.45 | 0.73 | 32 | empty |
| 3 | 116 | 0.38 | 0.74 | 18 | empty |
| 4 | 124 | 0.37 | 0.73 | 17 | empty |
| 5 | 103 | 0.37 | 0.74 | 15 | empty |
Interfaces
8 interfaces between chains.
- I–M · 48 Ų buried · 0 hydrogen bonds · protein-protein
- C–G · 44 Ų buried · 0 hydrogen bonds · protein-protein
- A–E · 43 Ų buried · 0 hydrogen bonds · protein-protein
- L–P · 43 Ų buried · 0 hydrogen bonds · protein-protein
- J–N · 43 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1WPB · Structure of Escherichia coli yfbU gene product · 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 Q1R9C1
- Elsewhere: RCSB PDB 1WPB · PDBe 1WPB · UniProt Q1R9C1
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