MolNFT v1 · #159731 · protein + DNA
Crystal structure of thermotoga maritima (tm) endonuclease V (D110N) in complex with a 12MER DNA containing an inosine followed by a ribo- adenosine
6OZF: “Crystal structure of thermotoga maritima (tm) endonuclease V (D110N) in complex with a 12MER DNA containing…”. X-ray diffraction, 2 ligands (CA, NA), 6 pockets (best druggability 0.66). MolNFT v1 #159731 on GenesisL1: 3D structure…
- PDB
- 6OZF
- Type
- protein + DNA
- Length
- 468 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endonuclease V; DNA/RNA (5'-D(P*AP*AP*TP*GP*I)-R(P*A)- D(P*GP*AP*TP*GP*CP*T)-3')
- EC
- 3.1.21.7
- UniProt
- Q9X2H9
- Ligands
- CA, NA
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endonuclease V (EC 3.1.21.7) | protein | 221 | 28% helix, 29% strand | Q9X2H9 |
| B | Endonuclease V (EC 3.1.21.7) | protein | 225 | 28% helix, 27% strand | Q9X2H9 |
| C | DNA/RNA (5'-D(P*AP*AP*TP*GP*I)-R(P*A)- D(P*GP*AP*TP*GP*CP*T)-3') | dna | 10 | — | — |
| D | DNA/RNA (5'-D(P*AP*AP*TP*GP*I)-R(P*A)- D(P*GP*AP*TP*GP*CP*T)-3') | dna | 12 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, C, B, D
- NA · Sodium ion · metal · 2 copies · chains A, C, B, D
- GOL · Glycerol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, A, C
- PG4 · Tetraethylene glycol · additive · chains A, B
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 | 436 | 0.66 | 0.78 | 39 | empty |
| 2 | 88 | 0.41 | 0.78 | 19 | CA |
| 3 | 111 | 0.39 | 0.76 | 19 | CA |
| 4 | 115 | 0.35 | 0.73 | 20 | empty |
| 5 | 91 | 0.34 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–D · 747 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 724 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–B · 550 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6OZF · Crystal structure of Thermotoga maritima (Tm) Endonuclease V (D110N) in complex with a… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9X2H9 · AlphaFold monomer V2.0 prediction for endonuclease V (Q9X2H9) · a predicted model of the same protein · 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
- Every structure of UniProt Q9X2H9
- Elsewhere: RCSB PDB 6OZF · PDBe 6OZF · UniProt Q9X2H9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.