Research workbench
Crystal structure of thermotoga maritima (tm) endonuclease V (E89Q) in complex with a 12MER DNA containing an inosine followed by a ribo- adenosine
Analyse Crystal structure of thermotoga maritima (tm) endonuclease V (E89Q) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OZG
- Type
- protein + DNA
- Length
- 464 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease V; DNA/RNA (5'-D(*AP*AP*TP*GP*A)-R(P*A)-D(P*GP*AP*T)- R(P*NP*N)-D(P*T)-3')
- EC
- 3.1.21.7
- UniProt
- Q9X2H9
- Ligands
- MG
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease V (EC 3.1.21.7) | protein | 222 | 27% helix, 26% strand | Q9X2H9 |
| B | Endonuclease V (EC 3.1.21.7) | protein | 224 | 29% helix, 27% strand | Q9X2H9 |
| C | DNA/RNA (5'-D(*AP*AP*TP*GP*A)-R(P*A)-D(P*GP*AP*T)- R(P*NP*N)-D(P*T)-3') | dna | 8 | — | — |
| D | DNA/RNA (5'-D(*AP*AP*TP*GP*A)-R(P*A)-D(P*GP*AP*T)- R(P*NP*N)-D(P*T)-3') | dna | 10 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains B, C, A
- GOL · Glycerol · additive · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 392 | 0.62 | 0.77 | 42 | GOL |
| 2 | 56 | 0.46 | 0.84 | 14 | empty |
| 3 | 64 | 0.41 | 0.81 | 15 | MG |
| 4 | 113 | 0.38 | 0.75 | 17 | empty |
| 5 | 100 | 0.35 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–D · 750 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–C · 725 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–B · 553 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6OZG · Crystal structure of Thermotoga maritima (Tm) Endonuclease V (E89Q) in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X2H9 · AlphaFold monomer V2.0 prediction for endonuclease V (Q9X2H9) · a predicted model of the same protein · chain B 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 Q9X2H9
- Elsewhere: RCSB PDB 6OZG · PDBe 6OZG · UniProt Q9X2H9
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