Research workbench
Leishmania naiffi uracil-DNA glycosylase in complex with 5-bromouracil
Analyse Leishmania naiffi uracil-DNA glycosylase in complex with 5-bromouracil in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CXM
- Type
- protein
- Length
- 242 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil-DNA glycosylase
- EC
- 3.2.2.-
- Ligands
- URB, URA, BR
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uracil-DNA glycosylase (EC 3.2.2.-) | protein | 242 | 39% helix, 10% strand | — |
Ligands and binding sites
- URB · 5-bromopyrimidine-2,4(1H,3H)-dione · ligand · chains A
- URA · Uracil · ligand · chains A
- BR · Bromide ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.43 | 0.77 | 18 | BR, URB, URA |
| 2 | 52 | 0.30 | 0.75 | 14 | empty |
Compared structures
- 3CXM · Leishmania naiffi uracil-DNA glycosylase in complex with 5-bromouracil · 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
- Elsewhere: RCSB PDB 3CXM · PDBe 3CXM
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