MolNFT v1 · #47678 · protein + DNA
Crystal structure of RB69 GP43 in complex with DNA containing an abasic site analog
2P5O · Template DNA: “Crystal structure of RB69 GP43 in complex with DNA containing an abasic site analog”. X-ray diffraction, 20 pockets (best druggability 0.82). MolNFT v1 #47678 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2P5O
- Type
- protein + DNA
- Length
- 3,262 residues
- Chains
- 12
- 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
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 9 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, I | Template DNA | dna | 18 | — | — |
| F, H, J | Primer DNA | dna | 15 | — | — |
| G | Template DNA | dna | 13 | — | — |
| K | Template DNA | dna | 9 | — | — |
| L | Primer DNA | dna | 8 | — | — |
| A | DNA polymerase (EC 2.7.7.7) | protein | 856 | 42% helix, 19% strand | Q38087 |
| B | DNA polymerase (EC 2.7.7.7) | protein | 771 | 40% helix, 16% strand | Q38087 |
| C | DNA polymerase (EC 2.7.7.7) | protein | 853 | 42% helix, 18% strand | Q38087 |
| D | DNA polymerase (EC 2.7.7.7) | protein | 671 | 39% helix, 11% strand | Q38087 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.82 | 0.92 | 41 | empty |
| 2 | 279 | 0.82 | 0.94 | 31 | empty |
| 3 | 1123 | 0.82 | 0.83 | 93 | empty |
| 4 | 800 | 0.77 | 0.81 | 68 | empty |
| 5 | 796 | 0.66 | 0.74 | 86 | empty |
Interfaces
16 interfaces between chains.
- I–C · 1132 Ų buried · 19 hydrogen bonds · protein-nucleic
- E–A · 999 Ų buried · 15 hydrogen bonds · protein-nucleic
- J–C · 800 Ų buried · 17 hydrogen bonds · protein-nucleic
- E–F · 692 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- I–J · 666 Ų buried · 53 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 97 modified (engineered, nucleotide modification).
Compared structures
- 2P5O · Crystal structure of RB69 GP43 in complex with DNA containing an abasic site analog · the same entry in another collection · chain E against E, 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 2P5O · PDBe 2P5O · UniProt Q38087
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.