MolNFT v1 · #47477 · protein + DNA
Crystal structure of RB69 GP43 in complex with DNA with datp opposite dtmp
2OZS · Template DNA: “Crystal structure of RB69 GP43 in complex with DNA with datp opposite dtmp”. X-ray diffraction, 2 ligands (DTP, MG), 13 pockets (best druggability 0.82). MolNFT v1 #47477 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2OZS
- Type
- protein + DNA
- Length
- 935 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Template DNA; Primer DNA; DNA polymerase
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- DTP, MG
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Template DNA | dna | 18 | — | — |
| P | Primer DNA | dna | 14 | — | — |
| A | DNA polymerase (EC 2.7.7.7) | protein | 903 | 43% helix, 18% strand | Q38087 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains T, P, A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.82 | 0.92 | 34 | empty |
| 2 | 998 | 0.78 | 0.80 | 90 | MG, DTP |
| 3 | 1098 | 0.77 | 0.79 | 71 | empty |
| 4 | 128 | 0.61 | 0.85 | 19 | empty |
| 5 | 272 | 0.57 | 0.77 | 25 | empty |
Interfaces
3 interfaces between chains.
- T–A · 1119 Ų buried · 15 hydrogen bonds · protein-nucleic
- P–A · 689 Ų buried · 13 hydrogen bonds · protein-nucleic
- T–P · 643 Ų buried · 65 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2OZS · Crystal structure of RB69 gp43 in complex with DNA with dATP opposite dTMP · the same entry in another collection · chain T against T, 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 Q38087
- Elsewhere: RCSB PDB 2OZS · PDBe 2OZS · UniProt Q38087
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.