MolNFT v1 · #179444 · protein + DNA
Bst DNA polymerase I time-resolved structure, 25.5 hr post datp and dctp addition
7K5T · DNA (5'-D(P*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3'): “Bst DNA polymerase I time-resolved structure, 25.5 hr post datp and dctp addition”. X-ray diffraction, 2 ligands (DCP, SO4), 8 pockets (best druggability 0.71). MolNFT v1 #179444 on…
- PDB
- 7K5T
- Type
- protein + DNA
- Length
- 600 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- E1C9K5
- Ligands
- DCP, SO4
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 57% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | DNA (5'-D(P*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3') | dna | 10 | — | — |
| T | DNA (5'-D(P*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*C)-3') | dna | 13 | — | — |
| A | DNA polymerase I (EC 2.7.7.7) | protein | 577 | 57% helix, 14% strand | E1C9K5 |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · chains P, T, A
- SO4 · Sulfate ion · ion · 3 copies · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 905 | 0.71 | 0.76 | 65 | SO4, DCP |
| 2 | 389 | 0.69 | 0.81 | 42 | empty |
| 3 | 153 | 0.67 | 0.88 | 24 | empty |
| 4 | 270 | 0.62 | 0.80 | 28 | empty |
| 5 | 146 | 0.53 | 0.81 | 19 | empty |
Interfaces
3 interfaces between chains.
- T–A · 984 Ų buried · 14 hydrogen bonds · protein-nucleic
- P–A · 728 Ų buried · 20 hydrogen bonds · protein-nucleic
- P–T · 463 Ų buried · 44 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7K5T · Bst DNA polymerase I time-resolved structure, 25.5 hr post dATP and dCTP addition · the same entry in another collection · chain P against P, 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 E1C9K5
- Elsewhere: RCSB PDB 7K5T · PDBe 7K5T · UniProt E1C9K5
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