MolNFT v1 · #152763 · protein + DNA
Structure of 9N-I DNA polymerase incorporation with dt in the active site
6ISF: “Structure of 9N-I DNA polymerase incorporation with dt in the active site”. X-ray diffraction, 1 ligand (CA), 18 pockets (best druggability 0.76). MolNFT v1 #152763 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ISF
- Type
- protein + DNA
- Length
- 1,579 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase; DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*T)- 3'); DNA (5'…
- EC
- 2.7.7.7
- UniProt
- Q56366
- Ligands
- CA
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 757 | 41% helix, 22% strand | Q56366 |
| B | DNA polymerase (EC 2.7.7.7) | protein | 756 | 42% helix, 23% strand | Q56366 |
| C, E | DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*T)- 3') | dna | 15 | — | — |
| D, F | DNA (5'- D(*AP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') | dna | 18 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.76 | 0.81 | 59 | empty |
| 2 | 890 | 0.75 | 0.79 | 94 | CA |
| 3 | 1060 | 0.74 | 0.77 | 86 | empty |
| 4 | 88 | 0.73 | 0.96 | 26 | empty |
| 5 | 195 | 0.71 | 0.89 | 40 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1039 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–F · 1028 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 781 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–E · 742 Ų buried · 22 hydrogen bonds · protein-nucleic
- E–F · 673 Ų buried · 64 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
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 Q56366
- Elsewhere: RCSB PDB 6ISF · PDBe 6ISF · UniProt Q56366
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