Research workbench
Crystal structure of RB69 GP43 in complex with DNA with 5-nimp opposite an abasic site analog
Analyse Crystal structure of RB69 GP43 in complex with DNA with 5-nimp opposite an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OYQ
- Type
- protein + DNA
- Length
- 3,418 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
- Ligands
- N5P, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 11 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Template DNA | dna | 16 | — | — |
| F, J | Primer DNA | dna | 15 | — | — |
| G | Template DNA | dna | 11 | — | — |
| H | Primer DNA | dna | 14 | — | — |
| I | Template DNA | dna | 20 | — | — |
| K | Template DNA | dna | 12 | — | — |
| L | Primer DNA | dna | 13 | — | — |
| A | DNA polymerase (EC 2.7.7.7) | protein | 848 | 43% helix, 20% strand | Q38087 |
| B | DNA polymerase (EC 2.7.7.7) | protein | 756 | 42% helix, 18% strand | Q38087 |
| C | DNA polymerase (EC 2.7.7.7) | protein | 891 | 43% helix, 18% strand | Q38087 |
| D | DNA polymerase (EC 2.7.7.7) | protein | 807 | 43% helix, 14% strand | Q38087 |
Ligands and binding sites
- N5P · 1-{2-deoxy-5-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-5-nitro -1H-indole · ligand · 4 copies · chains I, J, A, K, L, C
- MG · Magnesium ion · metal · 2 copies · chains I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 258 | 0.82 | 0.95 | 31 | empty |
| 2 | 255 | 0.81 | 0.93 | 30 | empty |
| 3 | 814 | 0.80 | 0.83 | 91 | empty |
| 4 | 948 | 0.79 | 0.82 | 91 | empty |
| 5 | 954 | 0.77 | 0.80 | 79 | empty |
Interfaces
17 interfaces between chains.
- I–C · 1265 Ų buried · 20 hydrogen bonds · protein-nucleic
- J–C · 860 Ų buried · 21 hydrogen bonds · protein-nucleic
- F–A · 737 Ų buried · 13 hydrogen bonds · protein-nucleic
- E–F · 692 Ų buried · 75 hydrogen bonds · nucleic-nucleic
- I–J · 683 Ų buried · 73 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 2OYQ · Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP opposite an abasic site… · the same entry in another collection · chain B against B, 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 2OYQ · PDBe 2OYQ · UniProt Q38087
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