MolNFT v1 · #89811 · protein + DNA
Binary complex of bacillus DNA polymerase I large fragment E658A and duplex DNA
4E0D: “Binary complex of bacillus DNA polymerase I large fragment E658A and duplex DNA”. X-ray diffraction, 2 ligands (DCP, SO4), 8 pockets (best druggability 0.70). MolNFT v1 #89811 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4E0D
- Type
- protein + DNA
- Length
- 598 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q5KWC1
- Ligands
- DCP, SO4
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 580 | 55% helix, 13% strand | Q5KWC1 |
| B | DNA (5'-D(*CP*CP*TP*GP*AP*CP*TP*CP*(DOC))-3') | dna | 9 | — | — |
| C | DNA (5'-D(*CP*AP*TP*GP*GP*GP*AP*GP*TP*CP*AP*GP*G)-3') | dna | 9 | — | — |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.70 | 0.76 | 64 | SO4 |
| 2 | 336 | 0.70 | 0.83 | 41 | MPD |
| 3 | 282 | 0.70 | 0.85 | 31 | empty |
| 4 | 240 | 0.63 | 0.81 | 27 | empty |
| 5 | 97 | 0.45 | 0.80 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 868 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–B · 838 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–C · 408 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4E0D · Binary complex of Bacillus DNA Polymerase I Large Fragment E658A and duplex DNA · 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 Q5KWC1
- Elsewhere: RCSB PDB 4E0D · PDBe 4E0D · UniProt Q5KWC1
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