MolNFT v1 · #54424 · protein + DNA
Crystal structure of a DA:O-allylhydroxylamine-dc basepair in complex with fragment DNA polymerase I from bacillus stearothermophilus
2XO7: “Crystal structure of a DA:O-allylhydroxylamine-dc basepair in complex with fragment DNA polymerase I from…”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.70). MolNFT v1 #54424 on GenesisL1: 3D structure…
- PDB
- 2XO7
- Type
- protein + DNA
- Length
- 601 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I; 5'-D(*GP*AP*CP*CP*AP*TP*47C*CP*CP*T)-3'…
- EC
- 2.7.7.7
- UniProt
- C3IXT2
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I (EC 2.7.7.7) | protein | 580 | 55% helix, 14% strand | C3IXT2 |
| B | 5'-D(*GP*AP*CP*CP*AP*TP*47C*CP*CP*T)-3' | dna | 10 | — | — |
| C | 5'-D(*AP*GP*GP*AP*AP*TP*GP*GP*TP*CP*A)-3' | dna | 11 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.70 | 0.88 | 25 | empty |
| 2 | 390 | 0.68 | 0.81 | 45 | empty |
| 3 | 354 | 0.60 | 0.77 | 46 | SO4 |
| 4 | 138 | 0.52 | 0.80 | 19 | empty |
| 5 | 171 | 0.47 | 0.76 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 882 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–B · 792 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–C · 491 Ų buried · 43 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2XO7 · Crystal structure of a dA:O-allylhydroxylamine-dC basepair in complex with fragment DNA… · 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 C3IXT2
- Elsewhere: RCSB PDB 2XO7 · PDBe 2XO7 · UniProt C3IXT2
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