Research workbench
Crystal structure of RB69 GP43 in complex with DNA containing thymine glycol
Analyse Crystal structure of RB69 GP43 in complex with DNA containing thymine glycol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DY4
- Type
- protein + DNA
- Length
- 3,706 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*GP*(CTG) P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-3'…
- EC
- 2.7.7.7
- UniProt
- Q38087
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 8 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | 5'-D(*CP*GP*(CTG) P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-3' | dna | 17 | — | — |
| F | 5'-D(*GP*CP*GP*GP*CP*TP*GP*T*CP*AP*TP*TP*CP*CP*A)-3' | dna | 13 | — | — |
| G, I, K | 5'-D(*CP*GP*(CTG) P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-3' | dna | 18 | — | — |
| H, J, L | 5'-D(*GP*CP*GP*GP*CP*TP*GP*T*CP*AP*TP*TP*CP*CP*A)-3' | dna | 14 | — | — |
| A | DNA polymerase (EC 2.7.7.7) | protein | 902 | 41% helix, 18% strand | Q38087 |
| B | DNA polymerase (EC 2.7.7.7) | protein | 888 | 41% helix, 19% strand | Q38087 |
| C | DNA polymerase (EC 2.7.7.7) | protein | 900 | 43% helix, 18% strand | Q38087 |
| D | DNA polymerase (EC 2.7.7.7) | protein | 890 | 34% helix, 14% 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 | 435 | 0.84 | 0.92 | 41 | empty |
| 2 | 314 | 0.84 | 0.94 | 29 | empty |
| 3 | 804 | 0.81 | 0.84 | 69 | empty |
| 4 | 753 | 0.77 | 0.82 | 54 | empty |
| 5 | 900 | 0.76 | 0.79 | 65 | empty |
Interfaces
16 interfaces between chains.
- I–C · 1033 Ų buried · 17 hydrogen bonds · protein-nucleic
- E–A · 1026 Ų buried · 20 hydrogen bonds · protein-nucleic
- G–B · 1009 Ų buried · 15 hydrogen bonds · protein-nucleic
- K–D · 854 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–D · 759 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 102 modified (engineered, nucleotide modification).
Compared structures
- 2DY4 · Crystal structure of RB69 GP43 in complex with DNA containing Thymine Glycol · 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 2DY4 · PDBe 2DY4 · UniProt Q38087
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