Research workbench
Crystal structure of a replicative DNA polymerase bound to DNA containing thymine glycol
Analyse Crystal structure of a replicative DNA polymerase bound to DNA containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RMB
- Type
- protein + DNA
- Length
- 3,727 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA (5'-D(*CP*GP*CP*(CTG) P*GP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')…
- EC
- 2.7.7.7
- UniProt
- Q38087
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase (EC 2.7.7.7) | protein | 903 | 40% helix, 18% strand | Q38087 |
| C | DNA polymerase (EC 2.7.7.7) | protein | 900 | 44% helix, 18% strand | Q38087 |
| D | DNA polymerase (EC 2.7.7.7) | protein | 897 | 40% helix, 18% strand | Q38087 |
| E, G, I, K | DNA (5'-D(*CP*GP*CP*(CTG) P*GP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3') | dna | 18 | — | — |
| F, H, J, L | DNA (5'-D(*GP*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*CP*A)-3') | dna | 13 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains C
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 | 460 | 0.83 | 0.91 | 62 | empty |
| 2 | 431 | 0.83 | 0.91 | 48 | empty |
| 3 | 395 | 0.82 | 0.91 | 45 | empty |
| 4 | 320 | 0.82 | 0.92 | 34 | empty |
| 5 | 940 | 0.79 | 0.81 | 79 | empty |
Interfaces
17 interfaces between chains.
- C–I · 1226 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–G · 1151 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–E · 1140 Ų buried · 19 hydrogen bonds · protein-nucleic
- D–K · 1078 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–D · 800 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 3RMB · Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol · the same entry in another collection · chain A against A, 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 3RMB · PDBe 3RMB · UniProt Q38087
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