Research workbench
Crystal structure of URE3-bp from entomaeba histolytica without calcium
Analyse Crystal structure of URE3-bp from entomaeba histolytica without calcium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q04
- Type
- protein
- Length
- 426 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- URE3-bp sequence specific DNA binding protein
- UniProt
- Q9GSV7
- Ligands
- NA, MG, SO4
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | URE3-bp sequence specific DNA binding protein | protein | 212 | 60% helix, 5% strand | Q9GSV7 |
| B | URE3-bp sequence specific DNA binding protein | protein | 214 | 60% helix, 5% strand | Q9GSV7 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.61 | 0.91 | 25 | empty |
| 2 | 111 | 0.56 | 0.84 | 27 | empty |
| 3 | 138 | 0.56 | 0.82 | 26 | empty |
| 4 | 227 | 0.55 | 0.78 | 40 | empty |
| 5 | 107 | 0.39 | 0.76 | 18 | GOL |
Interfaces
1 interface between chains.
- A–B · 1477 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4Q04 · Crystal structure of URE3-BP from Entomaeba histolytica without calcium · 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 Q9GSV7
- Elsewhere: RCSB PDB 4Q04 · PDBe 4Q04 · UniProt Q9GSV7
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