Research workbench
Crystal structure of RB69 GP43 in complex with DNA containing an abasic site analog
Analyse Crystal structure of RB69 GP43 in complex with DNA containing an abasic site… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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.