Research workbench
Crystal structure of RB69 GP43 in complex with DNA with damp opposite an abasic site analog in a 21MER template
Analyse Crystal structure of RB69 GP43 in complex with DNA with damp opposite an abasic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P5G
- Type
- protein + DNA
- Length
- 3,521 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 · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Template DNA | dna | 15 | — | — |
| F, H, J | Primer DNA | dna | 15 | — | — |
| G, K | Template DNA | dna | 11 | — | — |
| I | Template DNA | dna | 20 | — | — |
| L | Primer DNA | dna | 13 | — | — |
| A | DNA polymerase (EC 2.7.7.7) | protein | 890 | 43% helix, 19% strand | Q38087 |
| B | DNA polymerase (EC 2.7.7.7) | protein | 756 | 43% helix, 18% strand | Q38087 |
| C | DNA polymerase (EC 2.7.7.7) | protein | 885 | 42% helix, 19% strand | Q38087 |
| D | DNA polymerase (EC 2.7.7.7) | protein | 875 | 39% helix, 16% 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 | 240 | 0.82 | 0.95 | 27 | empty |
| 2 | 284 | 0.81 | 0.93 | 33 | empty |
| 3 | 1082 | 0.80 | 0.81 | 90 | empty |
| 4 | 510 | 0.80 | 0.87 | 39 | empty |
| 5 | 670 | 0.77 | 0.82 | 65 | empty |
Interfaces
17 interfaces between chains.
- I–C · 1230 Ų buried · 17 hydrogen bonds · protein-nucleic
- J–C · 837 Ų buried · 18 hydrogen bonds · protein-nucleic
- F–A · 717 Ų buried · 12 hydrogen bonds · protein-nucleic
- H–B · 678 Ų buried · 15 hydrogen bonds · protein-nucleic
- I–J · 667 Ų buried · 77 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 95 modified (engineered, nucleotide modification).
Compared structures
- 2P5G · Crystal structure of RB69 gp43 in complex with DNA with dAMP opposite an abasic site… · 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 2P5G · PDBe 2P5G · UniProt Q38087
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