Research workbench
Crystal structure of E159Q mutant of btucdf
Analyse Crystal structure of E159Q mutant of btucdf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DBL
- Type
- protein
- Length
- 2,778 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin B12 import system permease protein btuc; Vitamin B12 import ATP-binding protein…
- EC
- 3.6.3.33
- UniProt
- P06609, P06611, P37028
- Ligands
- SO4, PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F, G | Vitamin B12 import system permease protein btuc | protein | 324 | 76% helix, 0% strand | P06609 |
| C, D, H, I | Vitamin B12 import ATP-binding protein btud (EC 3.6.3.33) | protein | 248 | 38% helix, 29% strand | P06611 |
| E, J | Vitamin B12-binding protein | protein | 245 | 43% helix, 15% strand | P37028 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains C, D, H, I
- PO4 · Phosphate ion · ion · 4 copies · chains C, D, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.88 | 0.89 | 113 | empty |
| 2 | 1137 | 0.88 | 0.89 | 109 | empty |
| 3 | 1051 | 0.83 | 0.84 | 111 | PO4 |
| 4 | 1126 | 0.83 | 0.84 | 112 | PO4 |
| 5 | 822 | 0.81 | 0.84 | 81 | empty |
Interfaces
17 interfaces between chains.
- F–G · 1938 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1929 Ų buried · 9 hydrogen bonds · protein-protein
- F–J · 1419 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 1415 Ų buried · 15 hydrogen bonds · protein-protein
- G–J · 1352 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
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 P06609
- Every structure of UniProt P06611
- Every structure of UniProt P37028
- Elsewhere: RCSB PDB 4DBL · PDBe 4DBL · UniProt P06609 · UniProt P06611 · UniProt P37028
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