Research workbench
Crystal structure of methanocaldococcus jannaschii 8-oxoguanine GLYCOSYLASE/LYASE in complex with 15MER DNA containing 8-oxoguanine
Analyse Crystal structure of methanocaldococcus jannaschii 8-oxoguanine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KNT
- Type
- protein + DNA
- Length
- 938 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-GLYCOSYLASE/DNA lyase; 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3'…
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- Q58134
- Ligands
- NA
- Pockets
- 16 · best druggability 0.67
Structure
x-ray diffraction · 8 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 207 | 69% helix, 0% strand | Q58134 |
| C | N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 205 | 71% helix, 0% strand | Q58134 |
| D | N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 206 | 70% helix, 0% strand | Q58134 |
| E, K | 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3' | dna | 15 | — | — |
| F, L | 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3' | dna | 15 | — | — |
| G | 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3' | dna | 13 | — | — |
| H, J | 5'-D(*TP*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3' | dna | 13 | — | — |
| I | 5'-D(*AP*CP*GP*TP*CP*CP*AP*(8OG)P*GP*TP*CP*TP*AP*CP*C)-3' | dna | 14 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, E, B, G, C, I, D, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.67 | 0.76 | 51 | empty |
| 2 | 550 | 0.64 | 0.76 | 37 | empty |
| 3 | 453 | 0.62 | 0.77 | 34 | empty |
| 4 | 418 | 0.61 | 0.76 | 34 | empty |
| 5 | 301 | 0.53 | 0.75 | 25 | empty |
Interfaces
21 interfaces between chains.
- A–E · 849 Ų buried · 34 hydrogen bonds · protein-nucleic
- B–G · 840 Ų buried · 31 hydrogen bonds · protein-nucleic
- C–I · 833 Ų buried · 38 hydrogen bonds · protein-nucleic
- D–K · 823 Ų buried · 30 hydrogen bonds · protein-nucleic
- K–L · 649 Ų buried · 59 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 3KNT · Crystal structure of Methanocaldococcus jannaschii 8-oxoguanine glycosylase/lyase in… · the same entry in another collection · chain L against L, 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 Q58134
- Elsewhere: RCSB PDB 3KNT · PDBe 3KNT · UniProt Q58134
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