Research workbench
Crystal structure of E. COLI yfbu at 2.5 a resolution
Analyse Crystal structure of E. COLI yfbu at 2.5 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LR3
- Type
- protein
- Length
- 2,624 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein yfbu
- UniProt
- E2QPF5
- Ligands
- MG, PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 62% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P | Protein yfbu | protein | 164 | 62% helix, 2% strand | E2QPF5 |
Ligands and binding sites
- MG · Magnesium ion · metal · 32 copies · chains A, D, B, C, H, E, F, G, I, L, J, K, P, M, N, O
- PO4 · Phosphate ion · ion · 23 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
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.83 | 0.86 | 102 | MG |
| 2 | 1104 | 0.82 | 0.83 | 122 | MG |
| 3 | 923 | 0.73 | 0.77 | 107 | empty |
| 4 | 378 | 0.65 | 0.79 | 40 | empty |
| 5 | 384 | 0.65 | 0.79 | 40 | empty |
Interfaces
38 interfaces between chains.
- A–D · 1203 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 1180 Ų buried · 17 hydrogen bonds · protein-protein
- M–N · 1173 Ų buried · 18 hydrogen bonds · protein-protein
- I–L · 1170 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1169 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4LR3 · Crystal structure of E. coli YfbU at 2.5 A resolution · the same entry in another collection · chain O against O, 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 E2QPF5
- Elsewhere: RCSB PDB 4LR3 · PDBe 4LR3 · UniProt E2QPF5
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