MolNFT v1 · #152755 · protein + DNA
Structure of 9N-I DNA polymerase incorporation with da in the active site
6IS7: “Structure of 9N-I DNA polymerase incorporation with da in the active site”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.78). MolNFT v1 #152755 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IS7
- Type
- protein + DNA
- Length
- 1,590 residues
- Chains
- 9
- 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*A)- 3'); DNA (5'…
- EC
- 2.7.7.7
- UniProt
- Q56366
- Ligands
- CA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 7 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase (EC 2.7.7.7) | protein | 757 | 41% helix, 23% 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*A)- 3') | dna | 15 | — | — |
| D, F | DNA (5'- D(*AP*CP*TP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') | dna | 18 | — | — |
| I | DNA (5'- D(*AP*CP*TP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') | dna | 4 | — | — |
| K | DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*A)- 3') | dna | 3 | — | — |
| L | DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*A)- 3') | dna | 4 | — | — |
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
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 924 | 0.78 | 0.80 | 84 | empty |
| 2 | 381 | 0.73 | 0.84 | 44 | empty |
| 3 | 56 | 0.73 | 0.98 | 17 | empty |
| 4 | 499 | 0.72 | 0.81 | 47 | empty |
| 5 | 161 | 0.70 | 0.90 | 32 | empty |
Interfaces
10 interfaces between chains.
- B–F · 1085 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–D · 1075 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–C · 742 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–E · 738 Ų buried · 24 hydrogen bonds · protein-nucleic
- E–F · 677 Ų buried · 62 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 6IS7 · PDBe 6IS7 · UniProt Q56366
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