MolNFT v1 · #75667 · protein + DNA
Crystal structure of bacillus DNA polymerase I large fragment bound to DNA and ddctp-da mismatch (wobble) in ajar conformation
3PX4: “Crystal structure of bacillus DNA polymerase I large fragment bound to DNA and ddctp-da mismatch (wobble) in…”. X-ray diffraction, 3 ligands (DCT, MG, SO4), 20 pockets (best druggability 0.75). MolNFT v1 #75667 on GenesisL1: 3D…
- PDB
- 3PX4
- Type
- protein + DNA
- Length
- 1,167 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase I; DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q5KWC1
- Ligands
- DCT, MG, SO4
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase I (EC 2.7.7.7) | protein | 549 | 52% helix, 14% strand | Q5KWC1 |
| D | DNA polymerase I (EC 2.7.7.7) | protein | 579 | 55% helix, 13% strand | Q5KWC1 |
| B, E | DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3') | dna | 9 | — | — |
| C | DNA (5'-D(*CP*AP*TP*AP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3') | dna | 9 | — | — |
| F | DNA (5'-D(*CP*AP*TP*AP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · 2 copies · chains A, D, E, F
- MG · Magnesium ion · metal · chains D
- SO4 · Sulfate ion · ion · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.75 | 0.79 | 69 | DCT, MG |
| 2 | 506 | 0.72 | 0.81 | 47 | empty |
| 3 | 311 | 0.68 | 0.83 | 42 | empty |
| 4 | 374 | 0.68 | 0.81 | 40 | empty |
| 5 | 370 | 0.67 | 0.81 | 45 | empty |
Interfaces
7 interfaces between chains.
- D–F · 1243 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–C · 897 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–B · 803 Ų buried · 22 hydrogen bonds · protein-nucleic
- D–E · 766 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–D · 626 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3PX4 · Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddCTP-dA… · 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 Q5KWC1
- Elsewhere: RCSB PDB 3PX4 · PDBe 3PX4 · UniProt Q5KWC1
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