Research workbench
Crystal structure of uracil-DNA glycosylase from cod (gadus morhua) in complex with the proteinaceous inhibitor ugi
Analyse Crystal structure of uracil-DNA glycosylase from cod (gadus morhua) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LYL
- Type
- protein
- Length
- 2,440 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil-DNA glycosylase; Uracil-DNA glycosylase inhibitor
- EC
- 3.2.2.3
- UniProt
- Q9I983, P14739
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O | Uracil-DNA glycosylase (EC 3.2.2.3) | protein | 223 | 39% helix, 11% strand | Q9I983 |
| B, D, F, H, J, L, N, P | Uracil-DNA glycosylase inhibitor | protein | 82 | 21% helix, 40% strand | P14739 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.82 | 0.84 | 111 | empty |
| 2 | 822 | 0.78 | 0.81 | 80 | empty |
| 3 | 702 | 0.78 | 0.83 | 76 | empty |
| 4 | 784 | 0.78 | 0.82 | 84 | empty |
| 5 | 59 | 0.73 | 0.99 | 25 | empty |
Interfaces
29 interfaces between chains.
- G–H · 1113 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1107 Ų buried · 18 hydrogen bonds · protein-protein
- K–L · 1106 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1105 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1094 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4LYL · Crystal structure of uracil-DNA glycosylase from cod (Gadus morhua) in complex with the… · the same entry in another collection · chain B against B, 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 Q9I983
- Every structure of UniProt P14739
- Elsewhere: RCSB PDB 4LYL · PDBe 4LYL · UniProt Q9I983 · UniProt P14739
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.