4LYL: Uracil-DNA glycosylase from cod
Crystal structure of uracil-DNA glycosylase from cod (Gadus morhua) in complex with the proteinaceous inhibitor UGI. Determined by X-ray diffraction at 1.93 Å resolution. Released 13 Aug 2014.
- Method
- X-ray diffraction
- Resolution
- 1.93 Å
- Organisms
- Gadus morhua, Bacillus phage PBS2
- Chains
- 16
- Atoms
- 21,002
- Mol. weight
- 278.16 kDa
- Released
- 13 Aug 2014
Explore 4LYL in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4LYL contains 131 α-helices and 88 β-strands across 16 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 13 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 87-97 | 11 | |
| α-helix | 100-115 | 16 | |
| β-strand | 118-119 | 2 | 1 |
| α-helix | 122-124 | 3 | |
| α-helix | 127-130 | 4 | |
| β-strand | 139-143 | 5 | 2 |
| α-helix | 165-167 | 3 | |
| α-helix | 168-180 | 13 | |
| α-helix | 193-196 | 4 | |
| β-strand | 200-204 | 5 | 2 |
| β-strand | 209-210 | 2 | 1 |
| α-helix | 222-236 | 15 | |
| α-helix | 240 | 1 | |
| β-strand | 241-245 | 5 | 2 |
| α-helix | 247-252 | 6 | |
| β-strand | 262-266 | 5 | 2 |
| α-helix | 274-276 | 3 | |
| α-helix | 283-294 | 12 | |
| α-helix | 296-299 | 4 | |
Chains B and L: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-12 | 9 | |
| β-strand | 20-24 | 5 | 3 |
| α-helix | 26-33 | 8 | |
| β-strand | 41-48 | 8 | 3 |
| β-strand | 53-60 | 8 | 3 |
| α-helix | 61 | 1 | |
| β-strand | 67-73 | 7 | 3 |
| β-strand | 79-83 | 5 | 3 |
Chain C: 15 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 87-93 | 7 | |
| α-helix | 94-98 | 5 | |
| α-helix | 100-115 | 16 | |
| β-strand | 118-119 | 2 | 4 |
| α-helix | 122-124 | 3 | |
| α-helix | 127-130 | 4 | |
| α-helix | 134-136 | 3 | |
| β-strand | 139-143 | 5 | 5 |
| α-helix | 165-167 | 3 | |
| α-helix | 168-180 | 13 | |
| α-helix | 193-196 | 4 | |
| β-strand | 200-204 | 5 | 5 |
| β-strand | 209-210 | 2 | 4 |
| α-helix | 222-236 | 15 | |
| α-helix | 240 | 1 | |
| β-strand | 241-245 | 5 | 5 |
| α-helix | 247-252 | 6 | |
| β-strand | 262-266 | 5 | 5 |
| α-helix | 274-276 | 3 | |
| α-helix | 283-293 | 11 | |
| α-helix | 297-299 | 3 | |
Chain D: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-12 | 9 | |
| β-strand | 18-24 | 7 | 6 |
| α-helix | 26-33 | 8 | |
| β-strand | 41-48 | 8 | 6 |
| β-strand | 53-60 | 8 | 6 |
| β-strand | 67-73 | 7 | 6 |
| β-strand | 79-83 | 5 | 6 |
Chain E: 14 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 87-98 | 12 | |
| α-helix | 100-115 | 16 | |
| β-strand | 118-119 | 2 | 7 |
| α-helix | 122-124 | 3 | |
| α-helix | 127-129 | 3 | |
| α-helix | 134-136 | 3 | |
| β-strand | 139-143 | 5 | 8 |
| α-helix | 165-167 | 3 | |
| α-helix | 168-180 | 13 | |
| α-helix | 193-197 | 5 | |
| β-strand | 200-204 | 5 | 8 |
| β-strand | 209-210 | 2 | 7 |
| α-helix | 222-236 | 15 | |
| β-strand | 241-245 | 5 | 8 |
| α-helix | 247-252 | 6 | |
| β-strand | 262-266 | 5 | 8 |
| α-helix | 271-273 | 3 | |
| α-helix | 274-278 | 5 | |
| α-helix | 283-292 | 10 | |
| α-helix | 296-299 | 4 | |
Chains F and H: 3 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-12 | 9 | |
| β-strand | 18-24 | 7 | 9 |
| α-helix | 26-33 | 8 | |
| β-strand | 41-48 | 8 | 9 |
| β-strand | 53-60 | 8 | 9 |
| α-helix | 61 | 1 | |
| β-strand | 67-73 | 7 | 9 |
| β-strand | 79-83 | 5 | 9 |
Chain G: 14 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 87-93 | 7 | |
| α-helix | 94-96 | 3 | |
| α-helix | 100-115 | 16 | |
| β-strand | 118-119 | 2 | 10 |
| α-helix | 122-124 | 3 | |
| α-helix | 127-129 | 3 | |
| α-helix | 134-136 | 3 | |
| β-strand | 139-143 | 5 | 11 |
| α-helix | 165-167 | 3 | |
| α-helix | 168-180 | 13 | |
| α-helix | 193-196 | 4 | |
| β-strand | 200-204 | 5 | 11 |
| β-strand | 209-210 | 2 | 10 |
| α-helix | 222-236 | 15 | |
| β-strand | 241-245 | 5 | 11 |
| α-helix | 246-252 | 7 | |
| β-strand | 262-266 | 5 | 11 |
| α-helix | 274-276 | 3 | |
| α-helix | 283-293 | 11 | |
| α-helix | 297-299 | 3 | |
Chain I: 13 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 87-97 | 11 | |
| α-helix | 100-115 | 16 | |
| β-strand | 118-119 | 2 | 13 |
| α-helix | 122-124 | 3 | |
| α-helix | 127-129 | 3 | |
| α-helix | 134-136 | 3 | |
| β-strand | 139-143 | 5 | 14 |
| α-helix | 165-167 | 3 | |
| α-helix | 168-180 | 13 | |
| α-helix | 193-196 | 4 | |
| β-strand | 200-204 | 5 | 14 |
| β-strand | 209-210 | 2 | 13 |
| α-helix | 222-236 | 15 | |
| β-strand | 241-245 | 5 | 14 |
| α-helix | 247-253 | 7 | |
| β-strand | 262-266 | 5 | 14 |
| α-helix | 274-276 | 3 | |
| α-helix | 283-293 | 11 | |
| α-helix | 297-299 | 3 | |
5 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Uracil-DNA glycosylase | A, C, E, G, I, K, M, O | protein | 223 | Gadus morhua | Q9I983 (AlphaFold model) |
| Uracil-DNA glycosylase inhibitor | B, D, F, H, J, L, N, P | protein | 84 | Bacillus phage PBS2 | P14739 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G, I, K, M, O), FASTA
>4LYL_1 Uracil-DNA glycosylase (chains A, C, E, G, I, K, M, O)
MEFFGETWRRELAAEFEKPYFKQLMSFVADERSRHTVYPPADQVYSWTEMCDIQDVKVVI
LGQDPYHGPNQAHGLCFSVQKPVPPPPSLVNIYKELCTDIDGFKHPGHGDLSGWAKQGVL
LLNAVLTVRAHQANSHKDRGWETFTDAVIKWLSVNREGVVFLLWGSYAHKKGATIDRKRH
HVLQAVHPSPLSAHRGFLGCKHFSKANGLLKLSGTEPINWRAL
Sequence of entity 2 (B, D, F, H, J, L, N, P), FASTA
>4LYL_2 Uracil-DNA glycosylase inhibitor (chains B, D, F, H, J, L, N, P)
MTNLSDIIEKETGKQLVIQESILMLPEEVEEVIGNKPESDILVHTAYDESTDENVMLLTS
DAPEYKPWALVIQDSNGENKIKML
Primary citation
Structural and biophysical analysis of interactions between cod and human uracil-DNA N-glycosylase (UNG) and UNG inhibitor (Ugi). Assefa, N.G., Niiranen, L., Johnson, K.A. et al. Acta Crystallogr D Biol Crystallogr (2014) 70:2093-2100. DOI 10.1107/S1399004714011699 · PubMed
Other PDB entries of the same protein (UniProt Q9I983 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1OKB 1.9 Å, crystal structure of Uracil-DNA glycosylase from Atlantic cod (Gadus morhua)
Browse structure collections
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