MolNFT v1 · #90957 · protein + DNA
Bacillus DNA polymerase I large fragment complex 2
4EZ9: “Bacillus DNA polymerase I large fragment complex 2”. X-ray diffraction, 2 ligands (D3T, SO4), 19 pockets (best druggability 0.76). MolNFT v1 #90957 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4EZ9
- Type
- protein + DNA
- Length
- 1,198 residues
- Chains
- 6
- 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*(2DT))-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q5KWC1
- Ligands
- D3T, SO4
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 578 | 54% helix, 13% strand | Q5KWC1 |
| D | DNA polymerase (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*(2DT))-3') | dna | 9 | — | — |
| C | DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3') | dna | 11 | — | — |
| F | DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*GP*TP*CP*AP*GP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- D3T · 2',3'-dideoxy-thymidine-5'-triphosphate · ligand · chains D, E, F
- SO4 · Sulfate ion · ion · 2 copies · chains A, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.76 | 0.79 | 65 | D3T |
| 2 | 732 | 0.74 | 0.79 | 56 | empty |
| 3 | 434 | 0.71 | 0.82 | 57 | empty |
| 4 | 202 | 0.67 | 0.86 | 28 | empty |
| 5 | 351 | 0.67 | 0.81 | 45 | empty |
Interfaces
7 interfaces between chains.
- D–F · 1237 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 1218 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–B · 810 Ų buried · 22 hydrogen bonds · protein-nucleic
- D–E · 783 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–D · 722 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4EZ9 · Bacillus DNA Polymerase I Large Fragment Complex 2 · 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 4EZ9 · PDBe 4EZ9 · UniProt Q5KWC1
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